diff --git a/CHANGELOG.md b/CHANGELOG.md
index 97098afdf5a..c7f985e4a60 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ Docs: https://docs.openclaw.ai
 ### Fixes
 
 - Matrix/mentions: keep room mention gating strict while accepting visible `@displayName` Matrix URI labels, so `requireMention` works for non-OpenClaw Matrix clients again. (#64796) Thanks @hclsys.
+- Doctor: warn when on-disk agent directories still exist under `~/.openclaw/agents/<id>/agent` but the matching `agents.list[]` entries are missing from config. (#65113) Thanks @neeravmakwana.
 
 ## 2026.4.11
 
diff --git a/src/commands/doctor-state-integrity.test.ts b/src/commands/doctor-state-integrity.test.ts
index 058e1373db9..0271d61c6a4 100644
--- a/src/commands/doctor-state-integrity.test.ts
+++ b/src/commands/doctor-state-integrity.test.ts
@@ -58,6 +58,17 @@ function stateIntegrityText(): string {
     .join("\n");
 }
 
+function createAgentDir(agentId: string, includeNestedAgentDir = true) {
+  const stateDir = process.env.OPENCLAW_STATE_DIR;
+  if (!stateDir) {
+    throw new Error("OPENCLAW_STATE_DIR is not set");
+  }
+  const targetDir = includeNestedAgentDir
+    ? path.join(stateDir, "agents", agentId, "agent")
+    : path.join(stateDir, "agents", agentId);
+  fs.mkdirSync(targetDir, { recursive: true });
+}
+
 const OAUTH_PROMPT_MATCHER = expect.objectContaining({
   message: expect.stringContaining("Create OAuth dir at"),
 });
@@ -144,6 +155,110 @@ describe("doctor state integrity oauth dir checks", () => {
     expect(stateIntegrityText()).toContain("CRITICAL: OAuth dir missing");
   });
 
+  it("warns about orphaned on-disk agent directories missing from agents.list", async () => {
+    createAgentDir("big-brain");
+    createAgentDir("cerebro");
+
+    const text = await runStateIntegrityText({
+      agents: {
+        list: [{ id: "main", default: true }],
+      },
+    });
+
+    expect(text).toContain("without a matching agents.list entry");
+    expect(text).toContain("Examples: big-brain, cerebro");
+    expect(text).toContain("config-driven routing, identity, and model selection will ignore them");
+  });
+
+  it("detects orphaned agent dirs even when the on-disk folder casing differs", async () => {
+    createAgentDir("Research");
+
+    const text = await runStateIntegrityText({
+      agents: {
+        list: [{ id: "main", default: true }],
+      },
+    });
+
+    expect(text).toContain("without a matching agents.list entry");
+    expect(text).toContain("Examples: Research (id research)");
+  });
+
+  it("ignores configured agent dirs and incomplete agent folders", async () => {
+    createAgentDir("main");
+    createAgentDir("ops");
+    createAgentDir("staging", false);
+
+    const text = await runStateIntegrityText({
+      agents: {
+        list: [{ id: "main", default: true }, { id: "ops" }],
+      },
+    });
+
+    expect(text).not.toContain("without a matching agents.list entry");
+    expect(text).not.toContain("Examples:");
+  });
+
+  it("warns when a case-mismatched agent dir does not resolve to the configured agent path", async () => {
+    createAgentDir("Research");
+
+    const realpathNative = fs.realpathSync.native.bind(fs.realpathSync);
+    const realpathSpy = vi
+      .spyOn(fs.realpathSync, "native")
+      .mockImplementation((target, options) => {
+        const targetPath = String(target);
+        if (targetPath.endsWith(`${path.sep}agents${path.sep}research${path.sep}agent`)) {
+          const error = new Error("ENOENT");
+          (error as NodeJS.ErrnoException).code = "ENOENT";
+          throw error;
+        }
+        return realpathNative(target, options);
+      });
+
+    try {
+      const text = await runStateIntegrityText({
+        agents: {
+          list: [{ id: "main", default: true }, { id: "research" }],
+        },
+      });
+
+      expect(text).toContain("without a matching agents.list entry");
+      expect(text).toContain("Examples: Research (id research)");
+    } finally {
+      realpathSpy.mockRestore();
+    }
+  });
+
+  it("does not warn when a case-mismatched dir resolves to the configured agent path", async () => {
+    createAgentDir("Research");
+
+    const realpathNative = fs.realpathSync.native.bind(fs.realpathSync);
+    const resolvedResearchAgentDir = realpathNative(
+      path.join(process.env.OPENCLAW_STATE_DIR ?? "", "agents", "Research", "agent"),
+    );
+    const realpathSpy = vi
+      .spyOn(fs.realpathSync, "native")
+      .mockImplementation((target, options) => {
+        const targetPath = String(target);
+        if (targetPath.endsWith(`${path.sep}agents${path.sep}research${path.sep}agent`)) {
+          return resolvedResearchAgentDir;
+        }
+        return realpathNative(target, options);
+      });
+
+    try {
+      const text = await runStateIntegrityText({
+        agents: {
+          list: [{ id: "main", default: true }, { id: "research" }],
+        },
+      });
+
+      expect(text).not.toContain("without a matching agents.list entry");
+      expect(text).not.toContain("Examples:");
+    } finally {
+      realpathSpy.mockRestore();
+    }
+  });
+
   it("detects orphan transcripts and offers archival remediation", async () => {
     const cfg: OpenClawConfig = {};
     setupSessionState(cfg, process.env, process.env.HOME ?? "");
diff --git a/src/commands/doctor-state-integrity.ts b/src/commands/doctor-state-integrity.ts
index ce85c2fe618..e24af7f2557 100644
--- a/src/commands/doctor-state-integrity.ts
+++ b/src/commands/doctor-state-integrity.ts
@@ -1,7 +1,7 @@
 import fs from "node:fs";
 import os from "node:os";
 import path from "node:path";
-import { resolveDefaultAgentId } from "../agents/agent-scope.js";
+import { listAgentEntries, resolveDefaultAgentId } from "../agents/agent-scope.js";
 import { listBundledChannelPluginIds } from "../channels/plugins/bundled-ids.js";
 import { hasBundledChannelPersistedAuthState } from "../channels/plugins/persisted-auth-state.js";
 import { formatCliCommand } from "../cli/command-format.js";
@@ -19,6 +19,7 @@ import {
 import type { OpenClawConfig } from "../config/types.openclaw.js";
 import { resolveRequiredHomeDir } from "../infra/home-dir.js";
 import { resolveMemoryBackendConfig } from "../memory-host-sdk/engine-storage.js";
+import { normalizeAgentId } from "../routing/session-key.js";
 import { parseAgentSessionKey } from "../sessions/session-key-utils.js";
 import { asNullableObjectRecord } from "../shared/record-coerce.js";
 import { normalizeOptionalLowercaseString } from "../shared/string-coerce.js";
@@ -59,6 +60,86 @@ function existsFile(filePath: string): boolean {
   }
 }
 
+type OrphanAgentDir = {
+  dirName: string;
+  agentId: string;
+};
+
+function tryResolveNativeRealPath(targetPath: string): string | null {
+  try {
+    return fs.realpathSync.native(targetPath);
+  } catch {
+    return null;
+  }
+}
+
+function isReachableConfiguredAgentDir(params: {
+  agentsRoot: string;
+  dirName: string;
+  agentId: string;
+}): boolean {
+  if (params.dirName === params.agentId) {
+    return true;
+  }
+  const rawDir = path.join(params.agentsRoot, params.dirName, "agent");
+  const normalizedDir = path.join(params.agentsRoot, params.agentId, "agent");
+  const rawRealPath = tryResolveNativeRealPath(rawDir);
+  const normalizedRealPath = tryResolveNativeRealPath(normalizedDir);
+  return rawRealPath !== null && rawRealPath === normalizedRealPath;
+}
+
+function formatOrphanAgentDirLabel(entry: OrphanAgentDir): string {
+  return entry.dirName === entry.agentId ? entry.agentId : `${entry.dirName} (id ${entry.agentId})`;
+}
+
+function formatOrphanAgentDirPreview(entries: OrphanAgentDir[], limit = 3): string {
+  const labels = entries.slice(0, limit).map(formatOrphanAgentDirLabel);
+  const remaining = entries.length - labels.length;
+  if (remaining > 0) {
+    return `${labels.join(", ")}, and ${remaining} more`;
+  }
+  return labels.join(", ");
+}
+
+function listOrphanAgentDirs(cfg: OpenClawConfig, stateDir: string): OrphanAgentDir[] {
+  const configuredIds = new Set<string>();
+  configuredIds.add(normalizeAgentId(resolveDefaultAgentId(cfg)));
+  for (const entry of listAgentEntries(cfg)) {
+    configuredIds.add(normalizeAgentId(entry.id));
+  }
+
+  const agentsRoot = path.join(stateDir, "agents");
+  try {
+    const entries = fs.readdirSync(agentsRoot, { withFileTypes: true });
+    return entries
+      .filter((entry) => entry.isDirectory())
+      .map((entry) => ({
+        dirName: entry.name,
+        agentId: normalizeAgentId(entry.name),
+      }))
+      .filter(({ dirName, agentId }) => {
+        const hasNestedAgentDir = existsDir(path.join(agentsRoot, dirName, "agent"));
+        if (!hasNestedAgentDir) {
+          return false;
+        }
+        if (!configuredIds.has(agentId)) {
+          return true;
+        }
+        return !isReachableConfiguredAgentDir({
+          agentsRoot,
+          dirName,
+          agentId,
+        });
+      })
+      .toSorted(
+        (left, right) =>
+          left.agentId.localeCompare(right.agentId) || left.dirName.localeCompare(right.dirName),
+      );
+  } catch {
+    return [];
+  }
+}
+
 function canWriteDir(dir: string): boolean {
   try {
     fs.accessSync(dir, fs.constants.W_OK);
@@ -718,6 +799,18 @@ export async function noteStateIntegrity(
     );
   }
 
+  const orphanAgentDirs = listOrphanAgentDirs(cfg, stateDir);
+  if (orphanAgentDirs.length > 0) {
+    warnings.push(
+      [
+        `- Found ${countLabel(orphanAgentDirs.length, "agent directory", "agent directories")} on disk without a matching agents.list entry.`,
+        "  These agents can still have sessions/auth state on disk, but config-driven routing, identity, and model selection will ignore them.",
+        `  Examples: ${formatOrphanAgentDirPreview(orphanAgentDirs)}`,
+        `  Restore the missing agents.list entries or remove stale dirs after confirming they are no longer needed: ${shortenHomePath(path.join(stateDir, "agents"))}`,
+      ].join("\n"),
+    );
+  }
+
   const store = loadSessionStore(storePath);
   const sessionPathOpts = resolveSessionFilePathOptions({ agentId, storePath });
   const entries = Object.entries(store).filter(([, entry]) => entry && typeof entry === "object");