Windows Malicious Software Removal Tool Not Working? Fix MSRT

The Windows Malicious Software Removal Tool (MSRT) is a built-in Microsoft security utility that scans and removes specific malware families. Normally, it runs quietly in the background through Windows Update. However, many users face issues where MSRT is not working, does not open, closes immediately, or appears to do nothing after launching.

Common Windows Malicious Software Removal Tool Problems

Users commonly report the following MSRT issues:

• MSRT does not open after typing mrt
• The tool closes immediately after launch
• Scan freezes or never completes
• MSRT runs silently with no visible window
• “This app can’t run on your PC” error
• mrt.exe missing from the System32 folder
• No scan results or confirmation after running

Each issue has a specific cause, and the fixes below address them one by one.

Fix 1: Run Windows Malicious Software Removal Tool as Administrator

This is the most important fix. MSRT needs elevated permissions to scan protected system areas.

Steps:

1. Press Windows + R
2. Type:mrt
3. Press Ctrl + Shift + Enter
4. Click Yes when prompted

If MSRT opens and starts scanning, the issue was permission-related.

Fix 2: Run MSRT Directly from the System32 Folder

If the Run command fails, the shortcut or registry entry may be broken.

Steps:

1. Open File Explorer
2. Go to:C:\Windows\System32
3. Locate mrt.exe
4. Right-click → Run as administrator

If MSRT runs from this location, the tool itself is fine.

Fix 3: Check if Antivirus or Security Policy Is Blocking MSRT

Some third-party antivirus programs silently block system-level tools like MSRT.

What to do:

• Temporarily disable third-party antivirus software
• Run MSRT again
• Re-enable antivirus after the scan

If you’re using a work or school computer, MSRT may be blocked by Group Policy, and manual fixes may not work.

Fix 4: Repair Corrupted Windows System Files (Very Common)

Corrupted system files often cause MSRT to crash or refuse to launch.

Steps:

1. Open Command Prompt as Administrator
2. Run:sfc /scannow
3. Wait for the scan to complete
4. Restart your PC

Try running MSRT again after reboot.

Fix 5: Use DISM to Restore the Windows Image

If SFC does not fix the issue, DISM can repair deeper system corruption.

Steps:

1. Open Command Prompt as Administrator
2. Run:DISM /Online /Cleanup-Image /RestoreHealth
3. Restart your system once finished

This step fixes Windows components that MSRT depends on.

Fix 6: Make Sure Windows Update Is Working Properly

MSRT is delivered and updated through Windows Update. If updates are broken, MSRT may not run correctly.

Steps:

1. Open Settings → Windows Update
2. Click Check for updates
3. Install all pending updates
4. Restart your PC

After updating, MSRT is automatically reinstalled if missing.

Fix 7: Reinstall Windows Malicious Software Removal Tool Manually

If mrt.exe is missing or corrupted, reinstall MSRT manually.

Steps:

1. Visit the official Microsoft website
2. Download the latest version of MSRT
3. Run the downloaded file as administrator

This does not affect your personal files or Windows settings.

Fix 8: Check the MSRT Log File to Confirm It Ran

Sometimes MSRT runs without showing any interface.

Log file location:

C:\Windows\Debug\mrt.log

Open the file using Notepad and check:

• Scan start and end times
• Malware detection results
• Any recorded errors

If the log updates, MSRT is working even if no window appears.

Fix 9: Run MSRT in Safe Mode

Some malware actively blocks security tools.

Steps:

1. Open Settings → System → Recovery
2. Restart into Advanced startup
3. Select Safe Mode
4. Run:mrt

Safe Mode prevents malicious processes from interfering.

MSRT Still Not Working? Quick Checks Before You Give Up

Before moving to alternative scanners, confirm the following:

• mrt.log updates after running the tool
• Windows Update service is enabled
• Your device is not managed by an organization
• Microsoft Defender is turned on
• No third-party security software is blocking system tools

If all checks pass and MSRT still fails, continue below.

What Windows Malicious Software Removal Tool Cannot Do

Even when MSRT works correctly, keep these limitations in mind:

• It does not provide real-time protection
• It does not replace antivirus software
• It only targets specific malware families
• It is not a full system security solution

Always keep Microsoft Defender Antivirus enabled for ongoing protection.

When to Use an Alternative Malware Scanner

If MSRT fails repeatedly or detects nothing but issues persist, use:

• Microsoft Defender Offline Scan
• Other trusted malware removal tools

This helps identify threats MSRT is not designed to remove.

FAQs Windows Malicious Software Removal Tool Not Working

Why does MSRT close immediately after opening?

This usually happens due to missing administrator permissions, corrupted system files, or antivirus interference.

Is Windows Malicious Software Removal Tool removed in Windows 11?

No. MSRT is still included in Windows 11 and is delivered through Windows Update.

Does MSRT run automatically?

Yes. MSRT runs silently during scheduled Windows updates unless manually launched.

Where can I see MSRT scan results?

Results are stored in: C:\Windows\Debug\mrt.log

Can antivirus software block MSRT?

Yes. Some third-party security tools block system-level scans by default.

If Windows Malicious Software Removal Tool is not working, the issue is usually caused by permission errors, Windows corruption, or update failures. Running MSRT as administrator, repairing system files, and ensuring Windows Update works correctly resolves the problem in most cases.

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This guide helps restore MSRT functionality without reinstalling Windows or losing data, making it safe and effective for both Windows 10 and Windows 11 users.