diff --git a/src/infra/heartbeat-runner.ts b/src/infra/heartbeat-runner.ts
index ac3471adf..9bd67c69f 100644
--- a/src/infra/heartbeat-runner.ts
+++ b/src/infra/heartbeat-runner.ts
@@ -462,13 +462,18 @@ export async function runHeartbeatOnce(opts: {
 
   // Skip heartbeat if HEARTBEAT.md exists but has no actionable content.
   // This saves API calls/costs when the file is effectively empty (only comments/headers).
-  // EXCEPTION: Don't skip for exec events - they have pending system events to process.
+  // EXCEPTION: Don't skip for exec events or cron jobs - they have pending system events to process.
   const isExecEventReason = opts.reason === "exec-event";
+  const isCronReason = opts.reason?.startsWith("cron:");
   const workspaceDir = resolveAgentWorkspaceDir(cfg, agentId);
   const heartbeatFilePath = path.join(workspaceDir, DEFAULT_HEARTBEAT_FILENAME);
   try {
     const heartbeatFileContent = await fs.readFile(heartbeatFilePath, "utf-8");
-    if (isHeartbeatContentEffectivelyEmpty(heartbeatFileContent) && !isExecEventReason) {
+    if (
+      isHeartbeatContentEffectivelyEmpty(heartbeatFileContent) &&
+      !isExecEventReason &&
+      !isCronReason
+    ) {
       emitHeartbeatEvent({
         status: "skipped",
         reason: "empty-heartbeat-file",