diff --git a/lib/entry-points.js b/lib/entry-points.js
index 56914e8848..a0432668d2 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -161696,6 +161696,15 @@ async function run3(actionState) {
         `The 'init' action should not be run in the same workflow as 'setup-codeql'.`
       );
     }
+    try {
+      fs29.unlinkSync(getCommandCacheFilePath(actionState.env));
+    } catch (e) {
+      if (e?.code !== "ENOENT") {
+        logger.warning(
+          `Cannot delete CLI-cache file ${getCommandCacheFilePath(actionState.env)}: ${e}`
+        );
+      }
+    }
     toolsInput = await getToolsInput(
       actionStateWithFeatures,
       repositoryProperties
diff --git a/src/cli/output-cache.ts b/src/cli/output-cache.ts
index 8bf8c27abe..2c15f4580d 100644
--- a/src/cli/output-cache.ts
+++ b/src/cli/output-cache.ts
@@ -43,7 +43,7 @@ export function resetCachedCodeQlVersion(): void {
  * Returns the path to the temporary file that backs the
  * on-disk cache of CLI responses between workflow steps.
  */
-function getCommandCacheFilePath(env: Env): string {
+export function getCommandCacheFilePath(env: Env): string {
   return path.join(getTemporaryDirectory(env), COMMAND_CACHE_FILENAME);
 }
 
diff --git a/src/init-action.ts b/src/init-action.ts
index 6b5ed392ef..10ac425c59 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -22,6 +22,7 @@ import {
   getTotalCacheSize,
   shouldRestoreCache,
 } from "./caching-utils";
+import { getCommandCacheFilePath } from "./cli/output-cache";
 import { CodeQL } from "./codeql";
 import { getConfigFileInput } from "./config/file";
 import { ComputedInput, getToolsInput } from "./config/inputs";
@@ -296,6 +297,18 @@ async function run(
       );
     }
 
+    // Delete the CLI output-cache file if it exists, to avoid
+    // accidentally reusing a stale version from a previous run.
+    try {
+      fs.unlinkSync(getCommandCacheFilePath(actionState.env));
+    } catch (e: any) {
+      if (e?.code !== "ENOENT") {
+        logger.warning(
+          `Cannot delete CLI-cache file ${getCommandCacheFilePath(actionState.env)}: ${e}`,
+        );
+      }
+    }
+
     // Get the computed `tools` input.
     toolsInput = await getToolsInput(
       actionStateWithFeatures,