diff --git a/extensions/ql-vscode/CHANGELOG.md b/extensions/ql-vscode/CHANGELOG.md
index 4ff96f90f03..d9f20b56e09 100644
--- a/extensions/ql-vscode/CHANGELOG.md
+++ b/extensions/ql-vscode/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ## [UNRELEASED]
 
+- Add `codeQL.runningQueries.ignoredWorkspaceFolders` setting. [#3617](https://github.com/github/vscode-codeql/pull/3617)
+
 ## 1.13.0 - 1 May 2024
 
 - Add Ruby support to the CodeQL Model Editor. [#3584](https://github.com/github/vscode-codeql/pull/3584)
diff --git a/extensions/ql-vscode/package.json b/extensions/ql-vscode/package.json
index 8e6368c0ed1..ea7637e9f1f 100644
--- a/extensions/ql-vscode/package.json
+++ b/extensions/ql-vscode/package.json
@@ -198,6 +198,11 @@
             "maximum": 1024,
             "description": "Number of threads for running queries."
           },
+          "codeQL.runningQueries.ignoredWorkspaceFolders": {
+            "type": "array",
+            "default": [],
+            "description": "Workspace folders to ignore."
+          },
           "codeQL.runningQueries.saveCache": {
             "type": "boolean",
             "default": false,
diff --git a/extensions/ql-vscode/src/common/vscode/workspace-folders.ts b/extensions/ql-vscode/src/common/vscode/workspace-folders.ts
index 5f5f926f233..8e8a1352a89 100644
--- a/extensions/ql-vscode/src/common/vscode/workspace-folders.ts
+++ b/extensions/ql-vscode/src/common/vscode/workspace-folders.ts
@@ -1,6 +1,7 @@
 import { dirname, join } from "path";
 import type { WorkspaceFolder } from "vscode";
 import { workspace } from "vscode";
+import { IGNORED_WORKSPACE_FOLDERS_SETTING } from "../../config";
 
 /** Returns true if the specified workspace folder is on the file system. */
 export function isWorkspaceFolderOnDisk(
@@ -9,10 +10,23 @@ export function isWorkspaceFolderOnDisk(
   return workspaceFolder.uri.scheme === "file";
 }
 
+export function isWorkspaceFolderIgnored(
+  workspaceFolder: WorkspaceFolder,
+): boolean {
+  const ignoredFolders =
+    IGNORED_WORKSPACE_FOLDERS_SETTING.getValue() as string[];
+  return ignoredFolders.some((ignoredFolder) =>
+    workspaceFolder.uri.fsPath.startsWith(ignoredFolder),
+  );
+}
+
 /** Gets all active workspace folders that are on the filesystem. */
 export function getOnDiskWorkspaceFoldersObjects() {
   const workspaceFolders = workspace.workspaceFolders ?? [];
-  return workspaceFolders.filter(isWorkspaceFolderOnDisk);
+  return workspaceFolders.filter(
+    (f: WorkspaceFolder) =>
+      isWorkspaceFolderOnDisk(f) && !isWorkspaceFolderIgnored(f),
+  );
 }
 
 /** Gets all active workspace folders that are on the filesystem. */
diff --git a/extensions/ql-vscode/src/config.ts b/extensions/ql-vscode/src/config.ts
index 82807531f75..aae1735ca0b 100644
--- a/extensions/ql-vscode/src/config.ts
+++ b/extensions/ql-vscode/src/config.ts
@@ -230,6 +230,10 @@ const TIMEOUT_SETTING = new Setting("timeout", RUNNING_QUERIES_SETTING);
 const MEMORY_SETTING = new Setting("memory", RUNNING_QUERIES_SETTING);
 const DEBUG_SETTING = new Setting("debug", RUNNING_QUERIES_SETTING);
 const MAX_PATHS = new Setting("maxPaths", RUNNING_QUERIES_SETTING);
+export const IGNORED_WORKSPACE_FOLDERS_SETTING = new Setting(
+  "ignoredWorkspaceFolders",
+  RUNNING_QUERIES_SETTING,
+);
 const RUNNING_TESTS_SETTING = new Setting("runningTests", ROOT_SETTING);
 const RESULTS_DISPLAY_SETTING = new Setting("resultsDisplay", ROOT_SETTING);
 const USE_EXTENSION_PACKS = new Setting(