diff --git a/forms/customscriptslistitem.ui b/forms/customscriptslistitem.ui
index 5784b442..c6040aa1 100644
--- a/forms/customscriptslistitem.ui
+++ b/forms/customscriptslistitem.ui
@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>129</width>
-    <height>30</height>
+    <height>34</height>
    </rect>
   </property>
   <property name="sizePolicy">
@@ -23,6 +23,20 @@
    <property name="bottomMargin">
     <number>4</number>
    </property>
+   <item>
+    <widget class="QToolButton" name="b_Choose">
+     <property name="toolTip">
+      <string>Choose a new filepath for this script</string>
+     </property>
+     <property name="text">
+      <string>...</string>
+     </property>
+     <property name="icon">
+      <iconset resource="../resources/images.qrc">
+       <normaloff>:/icons/folder.ico</normaloff>:/icons/folder.ico</iconset>
+     </property>
+    </widget>
+   </item>
    <item>
     <widget class="QLineEdit" name="lineEdit_filepath">
      <property name="minimumSize">
@@ -37,16 +51,9 @@
     </widget>
    </item>
    <item>
-    <widget class="QToolButton" name="b_Choose">
-     <property name="toolTip">
-      <string>Choose a new filepath for this script</string>
-     </property>
+    <widget class="QCheckBox" name="checkBox_Enable">
      <property name="text">
-      <string>...</string>
-     </property>
-     <property name="icon">
-      <iconset resource="../resources/images.qrc">
-       <normaloff>:/icons/folder.ico</normaloff>:/icons/folder.ico</iconset>
+      <string/>
      </property>
     </widget>
    </item>
diff --git a/include/config.h b/include/config.h
index f715e36c..8ce5e2d2 100644
--- a/include/config.h
+++ b/include/config.h
@@ -348,8 +348,11 @@ public:
     bool getEncounterJsonActive();
     void setProjectDir(QString projectDir);
     QString getProjectDir();
-    void setCustomScripts(QStringList scripts);
-    QStringList getCustomScripts();
+    void setCustomScripts(QStringList scripts, QList<bool> enabled);
+    QStringList getCustomScriptPaths();
+    QList<bool> getCustomScriptsEnabled();
+    void parseCustomScripts(QString input);
+    QString outputCustomScripts();
 protected:
     virtual QString getConfigFilepath() override;
     virtual void parseConfigKeyValue(QString key, QString value) override;
@@ -363,7 +366,7 @@ private:
     QString projectDir;
     QString recentMap;
     bool useEncounterJson;
-    QStringList customScripts;
+    QMap<QString, bool> customScripts;
     QStringList readKeys;
 };
 
diff --git a/include/ui/customscriptseditor.h b/include/ui/customscriptseditor.h
index 1d8b88c2..a2482fc3 100644
--- a/include/ui/customscriptseditor.h
+++ b/include/ui/customscriptseditor.h
@@ -31,16 +31,17 @@ private:
     QString importDir;
     const QString baseDir;
 
-    void displayScript(const QString &filepath);
+    void displayScript(const QString &filepath, bool enabled);
     QString chooseScript(QString dir);
 
     void removeScript(QListWidgetItem * item);
     void replaceScript(QListWidgetItem * item);
     void openScript(QListWidgetItem * item);
+    QString getScriptFilepath(QListWidgetItem * item, bool absolutePath = true) const;
+    void setScriptFilepath(QListWidgetItem * item, QString filepath) const;
+    bool getScriptEnabled(QListWidgetItem * item) const;
 
-    QString getListItemFilepath(QListWidgetItem * item) const;
-    void setListItemFilepath(QListWidgetItem * item, QString filepath) const;
-
+    void markEdited();
     int prompt(const QString &text, QMessageBox::StandardButton defaultButton);
     void save();
     void closeEvent(QCloseEvent*);
diff --git a/src/config.cpp b/src/config.cpp
index d5e7e0fe..6e2193f2 100644
--- a/src/config.cpp
+++ b/src/config.cpp
@@ -646,14 +646,7 @@ void ProjectConfig::parseConfigKeyValue(QString key, QString value) {
     } else if (key == "use_encounter_json") {
         userConfig.useEncounterJson = getConfigBool(key, value);
     } else if (key == "custom_scripts") {
-        userConfig.customScripts.clear();
-        QList<QString> paths = value.split(",", Qt::SkipEmptyParts);
-        paths.removeDuplicates();
-        for (QString script : paths) {
-            if (!script.isEmpty()) {
-                userConfig.customScripts.append(script);
-            }
-        }
+        userConfig.parseCustomScripts(value);
 #endif
     } else if (key.startsWith("path/")) {
         auto k = reverseDefaultPaths(key.mid(5));
@@ -1076,14 +1069,7 @@ void UserConfig::parseConfigKeyValue(QString key, QString value) {
     } else if (key == "use_encounter_json") {
         this->useEncounterJson = getConfigBool(key, value);
     } else if (key == "custom_scripts") {
-        this->customScripts.clear();
-        QList<QString> paths = value.split(",", Qt::SkipEmptyParts);
-        paths.removeDuplicates();
-        for (QString script : paths) {
-            if (!script.isEmpty()) {
-                this->customScripts.append(script);
-            }
-        }
+        this->parseCustomScripts(value);
     } else {
         logWarn(QString("Invalid config key found in config file %1: '%2'").arg(this->getConfigFilepath()).arg(key));
     }
@@ -1097,7 +1083,7 @@ QMap<QString, QString> UserConfig::getKeyValueMap() {
     QMap<QString, QString> map;
     map.insert("recent_map", this->recentMap);
     map.insert("use_encounter_json", QString::number(this->useEncounterJson));
-    map.insert("custom_scripts", this->customScripts.join(","));
+    map.insert("custom_scripts", this->outputCustomScripts());
     return map;
 }
 
@@ -1133,13 +1119,51 @@ bool UserConfig::getEncounterJsonActive() {
     return this->useEncounterJson;
 }
 
-void UserConfig::setCustomScripts(QStringList scripts) {
-    this->customScripts = scripts;
+// Read input from the config to get the script paths and whether each is enabled or disbled.
+// The format is a comma-separated list of paths. Each path can be followed (before the comma)
+// by a :0 or :1 to indicate whether it should be disabled or enabled, respectively. If neither
+// follow, it's assumed the script should be enabled.
+void UserConfig::parseCustomScripts(QString input) {
+    this->customScripts.clear();
+    QList<QString> paths = input.split(",", Qt::SkipEmptyParts);
+    for (QString path : paths) {
+        // Read and remove suffix
+        bool enabled = !path.endsWith(":0");
+        if (!enabled || path.endsWith(":1"))
+            path.chop(2);
+
+        if (!path.isEmpty()) {
+            // If a path is repeated only its last instance will be considered.
+            this->customScripts.insert(path, enabled);
+        }
+    }
+}
+
+// Inverse of UserConfig::parseCustomScripts
+QString UserConfig::outputCustomScripts() {
+    QStringList list;
+    QMapIterator<QString, bool> i(this->customScripts);
+    while (i.hasNext()) {
+        i.next();
+        list.append(QString("%1:%2").arg(i.key()).arg(i.value() ? "1" : "0"));
+    }
+    return list.join(",");
+}
+
+void UserConfig::setCustomScripts(QStringList scripts, QList<bool> enabled) {
+    this->customScripts.clear();
+    size_t size = qMin(scripts.length(), enabled.length());
+    for (size_t i = 0; i < size; i++)
+        this->customScripts.insert(scripts.at(i), enabled.at(i));
     this->save();
 }
 
-QStringList UserConfig::getCustomScripts() {
-    return this->customScripts;
+QStringList UserConfig::getCustomScriptPaths() {
+    return this->customScripts.keys();
+}
+
+QList<bool> UserConfig::getCustomScriptsEnabled() {
+    return this->customScripts.values();
 }
 
 ShortcutsConfig shortcutsConfig;
diff --git a/src/scriptapi/apiutility.cpp b/src/scriptapi/apiutility.cpp
index baeb2017..559e46af 100644
--- a/src/scriptapi/apiutility.cpp
+++ b/src/scriptapi/apiutility.cpp
@@ -184,7 +184,7 @@ bool ScriptUtility::getSmartPathsEnabled() {
 }
 
 QList<QString> ScriptUtility::getCustomScripts() {
-    return userConfig.getCustomScripts();
+    return userConfig.getCustomScriptPaths();
 }
 
 QList<int> ScriptUtility::getMetatileLayerOrder() {
diff --git a/src/scriptapi/scripting.cpp b/src/scriptapi/scripting.cpp
index 9aa6963c..5ff90d37 100644
--- a/src/scriptapi/scripting.cpp
+++ b/src/scriptapi/scripting.cpp
@@ -36,8 +36,11 @@ Scripting::Scripting(MainWindow *mainWindow) {
     this->mainWindow = mainWindow;
     this->engine = new QJSEngine(mainWindow);
     this->engine->installExtensions(QJSEngine::ConsoleExtension);
-    for (QString script : userConfig.getCustomScripts()) {
-        this->filepaths.append(script);
+    const QStringList paths = userConfig.getCustomScriptPaths();
+    const QList<bool> enabled = userConfig.getCustomScriptsEnabled();
+    for (int i = 0; i < paths.length(); i++) {
+        if (enabled.at(i))
+            this->filepaths.append(paths.at(i));
     }
     this->loadModules(this->filepaths);
     this->scriptUtility = new ScriptUtility(mainWindow);
diff --git a/src/ui/customscriptseditor.cpp b/src/ui/customscriptseditor.cpp
index 36babd51..c54ec1c7 100644
--- a/src/ui/customscriptseditor.cpp
+++ b/src/ui/customscriptseditor.cpp
@@ -8,8 +8,6 @@
 #include <QDir>
 #include <QFileDialog>
 
-// TODO: System for turning scripts on or off
-//
 // TODO: Better URL colors on dark themes
 // TODO: Save window state
 
@@ -23,8 +21,10 @@ CustomScriptsEditor::CustomScriptsEditor(QWidget *parent) :
     // This property seems to be reset if we don't set it programmatically
     ui->list->setDragDropMode(QAbstractItemView::NoDragDrop);
 
-    for (auto path : userConfig.getCustomScripts())
-        this->displayScript(path);
+    const QStringList paths = userConfig.getCustomScriptPaths();
+    const QList<bool> enabled = userConfig.getCustomScriptsEnabled();
+    for (int i = 0; i < paths.length(); i++)
+        this->displayScript(paths.at(i), enabled.at(i));
 
     this->importDir = userConfig.getProjectDir();
 
@@ -90,36 +90,44 @@ void CustomScriptsEditor::applyUserShortcuts() {
             shortcut->setKeys(shortcutsConfig.userShortcuts(shortcut));
 }
 
-void CustomScriptsEditor::displayScript(const QString &filepath) {
+void CustomScriptsEditor::displayScript(const QString &filepath, bool enabled) {
     auto item = new QListWidgetItem();
-    auto buttons = new CustomScriptsListItem();
+    auto widget = new CustomScriptsListItem();
 
-    buttons->ui->lineEdit_filepath->setText(filepath);
-    item->setSizeHint(buttons->sizeHint());
+    widget->ui->checkBox_Enable->setChecked(enabled);
+    widget->ui->lineEdit_filepath->setText(filepath);
+    item->setSizeHint(widget->sizeHint());
 
-    connect(buttons->ui->b_Choose, &QAbstractButton::clicked, [this, item](bool) { this->replaceScript(item); });
-    connect(buttons->ui->b_Edit,   &QAbstractButton::clicked, [this, item](bool) { this->openScript(item); });
-    connect(buttons->ui->b_Delete, &QAbstractButton::clicked, [this, item](bool) { this->removeScript(item); });
-    connect(buttons->ui->lineEdit_filepath, &QLineEdit::textEdited, [this](const QString&) { this->hasUnsavedChanges = true; });
+    connect(widget->ui->b_Choose, &QAbstractButton::clicked, [this, item](bool) { this->replaceScript(item); });
+    connect(widget->ui->b_Edit,   &QAbstractButton::clicked, [this, item](bool) { this->openScript(item); });
+    connect(widget->ui->b_Delete, &QAbstractButton::clicked, [this, item](bool) { this->removeScript(item); });
+    connect(widget->ui->checkBox_Enable, &QCheckBox::stateChanged, this, &CustomScriptsEditor::markEdited);
+    connect(widget->ui->lineEdit_filepath, &QLineEdit::textEdited, this, &CustomScriptsEditor::markEdited);
 
     // Per the Qt manual, for performance reasons QListWidget::setItemWidget shouldn't be used with non-static items.
     // There's an assumption here that users won't have enough scripts for that to be a problem.
     ui->list->addItem(item);
-    ui->list->setItemWidget(item, buttons);
+    ui->list->setItemWidget(item, widget);
 }
 
-QString CustomScriptsEditor::getListItemFilepath(QListWidgetItem * item) const {
+void CustomScriptsEditor::markEdited() {
+    this->hasUnsavedChanges = true;
+}
+
+QString CustomScriptsEditor::getScriptFilepath(QListWidgetItem * item, bool absolutePath) const {
     auto widget = dynamic_cast<CustomScriptsListItem *>(ui->list->itemWidget(item));
     if (!widget) return QString();
 
     QString path = widget->ui->lineEdit_filepath->text();
-    QFileInfo fileInfo(path);
-    if (fileInfo.isRelative())
-        path.prepend(this->baseDir);
+    if (absolutePath) {
+        QFileInfo fileInfo(path);
+        if (fileInfo.isRelative())
+            path.prepend(this->baseDir);
+    }
     return path;
 }
 
-void CustomScriptsEditor::setListItemFilepath(QListWidgetItem * item, QString filepath) const {
+void CustomScriptsEditor::setScriptFilepath(QListWidgetItem * item, QString filepath) const {
     auto widget = dynamic_cast<CustomScriptsListItem *>(ui->list->itemWidget(item));
     if (!widget) return;
 
@@ -128,6 +136,11 @@ void CustomScriptsEditor::setListItemFilepath(QListWidgetItem * item, QString fi
     widget->ui->lineEdit_filepath->setText(filepath);
 }
 
+bool CustomScriptsEditor::getScriptEnabled(QListWidgetItem * item) const {
+    auto widget = dynamic_cast<CustomScriptsListItem *>(ui->list->itemWidget(item));
+    return widget && widget->ui->checkBox_Enable->isChecked();
+}
+
 QString CustomScriptsEditor::chooseScript(QString dir) {
     return QFileDialog::getOpenFileName(this, "Choose Custom Script File", dir, "JavaScript Files (*.js)");
 }
@@ -139,13 +152,13 @@ void CustomScriptsEditor::addNewScript() {
     this->importDir = filepath;
     if (filepath.startsWith(this->baseDir))
         filepath.remove(0, this->baseDir.length());
-    this->displayScript(filepath);
-    this->hasUnsavedChanges = true;
+    this->displayScript(filepath, true);
+    this->markEdited();
 }
 
 void CustomScriptsEditor::removeScript(QListWidgetItem * item) {
     ui->list->takeItem(ui->list->row(item));
-    this->hasUnsavedChanges = true;
+    this->markEdited();
 }
 
 void CustomScriptsEditor::removeSelectedScripts() {
@@ -157,15 +170,15 @@ void CustomScriptsEditor::removeSelectedScripts() {
 }
 
 void CustomScriptsEditor::replaceScript(QListWidgetItem * item) {
-    const QString filepath = this->chooseScript(this->getListItemFilepath(item));
+    const QString filepath = this->chooseScript(this->getScriptFilepath(item));
     if (filepath.isEmpty())
         return;
-    this->setListItemFilepath(item, filepath);
-    this->hasUnsavedChanges = true;
+    this->setScriptFilepath(item, filepath);
+    this->markEdited();
 }
 
 void CustomScriptsEditor::openScript(QListWidgetItem * item) {
-    const QString path = this->getListItemFilepath(item);
+    const QString path = this->getScriptFilepath(item);
     QFileInfo fileInfo(path);
     if (!fileInfo.exists() || !fileInfo.isFile()){
         QMessageBox::warning(this, "", QString("Failed to open script '%1'").arg(path));
@@ -191,7 +204,16 @@ void CustomScriptsEditor::reloadScripts() {
 void CustomScriptsEditor::save() {
     if (!this->hasUnsavedChanges)
         return;
-    // TODO: Set new paths in config
+
+    QStringList paths;
+    QList<bool> enabledStates;
+    for (int i = 0; i < ui->list->count(); i++) {
+        auto item = ui->list->item(i);
+        paths.append(this->getScriptFilepath(item, false));
+        enabledStates.append(this->getScriptEnabled(item));
+    }
+
+    userConfig.setCustomScripts(paths, enabledStates);
     this->hasUnsavedChanges = false;
     this->reloadScripts();
 }