MCP Directory

title: "10 Most Common MCP Setup Errors (and Fixes)" description: "Troubleshoot the most common MCP setup errors with step-by-step solutions and prevention tips." slug: "common-errors" category: "testing" updatedAt: "2025-09-21T00:00:00.000Z" faqs:

  • q: "Why does my MCP server keep crashing?" a: "Common causes include memory leaks, unhandled exceptions, or resource exhaustion. Check logs and implement proper error handling."
  • q: "How do I fix 'MCP server not responding' errors?" a: "Check if the server process is running, verify network connectivity, and ensure the server isn't overloaded with requests."
Testing & Debugging
MCP SDK v2.1.0
Updated Sep 21, 20255 min read
errors
setup
troubleshooting

10 Most Common MCP Setup Errors (and Fixes)

Overview

This guide covers the 10 most common MCP setup errors encountered by developers, along with step-by-step solutions and prevention strategies.

1. Connection Refused Error

Error Message:

Error: connect ECONNREFUSED 127.0.0.1:3000

Cause: The MCP server is not running or not listening on the expected port.

Solution:

# Check if server is running
ps aux | grep mcp

# Check port usage
lsof -i :3000

# Start the server
npm start
# or
python -m mcp_server

Prevention:

  • Always verify server status before connecting
  • Use process managers like PM2 for production
  • Implement health check endpoints

2. Module Not Found Error

Error Message:

Error: Cannot find module '@modelcontextprotocol/sdk'

Cause: Missing dependencies or incorrect installation.

Solution:

# Install missing dependencies
npm install @modelcontextprotocol/sdk

# For Python
pip install mcp

# Clear cache and reinstall
npm cache clean --force
npm install

Prevention:

  • Always run npm install or pip install -r requirements.txt
  • Use lock files (package-lock.json, requirements.txt)
  • Verify Node.js/Python versions

3. Authentication Failed

Error Message:

Error: Authentication failed - invalid token

Cause: Missing, expired, or incorrect API tokens.

Solution:

# Set environment variable
export GITHUB_PERSONAL_ACCESS_TOKEN="your_token_here"

# Verify token
curl -H "Authorization: token $GITHUB_PERSONAL_ACCESS_TOKEN" https://api.github.com/user

# Generate new token if needed
# Go to GitHub Settings > Developer settings > Personal access tokens

Prevention:

  • Use environment variables for tokens
  • Implement token validation
  • Set up token rotation

4. Port Already in Use

Error Message:

Error: listen EADDRINUSE: address already in use :::3000

Cause: Another process is using the same port.

Solution:

# Find process using the port
lsof -i :3000

# Kill the process
kill -9 <PID>

# Or use a different port
MCP_PORT=3001 npm start

Prevention:

  • Use dynamic port allocation
  • Check port availability before starting
  • Use port management tools

5. Permission Denied

Error Message:

Error: EACCES: permission denied, open '/path/to/file'

Cause: Insufficient file system permissions.

Solution:

# Fix file permissions
chmod 644 /path/to/file
chmod 755 /path/to/directory

# Change ownership
chown user:group /path/to/file

# Run with appropriate user
sudo -u mcp npm start

Prevention:

  • Use proper user accounts
  • Set correct file permissions
  • Avoid running as root

6. Configuration File Not Found

Error Message:

Error: Configuration file not found: mcp.config.json

Cause: Missing or incorrectly located configuration file.

Solution:

# Create configuration file
cat > mcp.config.json << EOF
{
  "servers": {
    "filesystem": {
      "command": "node",
      "args": ["dist/index.js"]
    }
  }
}
EOF

# Specify config path
MCP_CONFIG_PATH=/path/to/mcp.config.json npm start

Prevention:

  • Use absolute paths for config files
  • Validate configuration on startup
  • Provide default configurations

7. Memory Limit Exceeded

Error Message:

Error: JavaScript heap out of memory

Cause: Insufficient memory allocation or memory leaks.

Solution:

# Increase Node.js memory limit
node --max-old-space-size=4096 dist/index.js

# For Docker
docker run -m 2g mcp-server

# Monitor memory usage
node --inspect dist/index.js

Prevention:

  • Implement proper memory management
  • Use streaming for large data
  • Monitor memory usage

8. SSL/TLS Certificate Error

Error Message:

Error: unable to verify the first certificate

Cause: Invalid or self-signed SSL certificates.

Solution:

# For development (not recommended for production)
export NODE_TLS_REJECT_UNAUTHORIZED=0

# Use proper certificates
openssl req -x509 -newkey rsa:4096 -keyout key.pem -out cert.pem -days 365

# Update certificate store
npm config set cafile /path/to/certificate.pem

Prevention:

  • Use valid SSL certificates
  • Keep certificates updated
  • Implement certificate validation

9. Timeout Error

Error Message:

Error: Request timeout after 30000ms

Cause: Server taking too long to respond or network issues.

Solution:

# Increase timeout
MCP_TIMEOUT=60000 npm start

# Check server performance
curl -w "@curl-format.txt" -o /dev/null -s http://localhost:3000/health

# Optimize server code
# - Add caching
# - Optimize database queries
# - Use connection pooling

Prevention:

  • Implement proper timeout handling
  • Optimize server performance
  • Use caching strategies

10. Version Compatibility Error

Error Message:

Error: Unsupported MCP protocol version

Cause: Version mismatch between client and server.

Solution:

# Check versions
npm list @modelcontextprotocol/sdk

# Update to compatible versions
npm update @modelcontextprotocol/sdk

# Use specific version
npm install @modelcontextprotocol/sdk@^2.0.0

Prevention:

  • Pin dependency versions
  • Test compatibility before updates
  • Maintain version compatibility matrix

Debugging Tools

Log Analysis

# Enable debug logging
DEBUG=mcp:* npm start

# Tail logs
tail -f /var/log/mcp/server.log

# Search logs
grep "ERROR" /var/log/mcp/server.log

Network Debugging

# Test connectivity
telnet localhost 3000

# Check DNS resolution
nslookup your-mcp-server.com

# Monitor network traffic
tcpdump -i any port 3000

Process Monitoring

# Monitor processes
htop

# Check system resources
free -h
df -h

# Monitor specific process
pidstat -p <PID> 1

Prevention Strategies

1. Comprehensive Testing

# Unit tests
npm test

# Integration tests
npm run test:integration

# Load testing
artillery run load-test.yml

2. Monitoring and Alerting

// Health check endpoint
app.get('/health', (req, res) => {
  const health = {
    status: 'healthy',
    timestamp: new Date().toISOString(),
    uptime: process.uptime(),
    memory: process.memoryUsage()
  };
  res.json(health);
});

3. Error Handling

// Global error handler
process.on('uncaughtException', (error) => {
  console.error('Uncaught Exception:', error);
  process.exit(1);
});

process.on('unhandledRejection', (reason, promise) => {
  console.error('Unhandled Rejection at:', promise, 'reason:', reason);
});

FAQ

Why does my MCP server keep crashing?

Common causes include memory leaks, unhandled exceptions, or resource exhaustion. Check your logs for error messages, implement proper error handling, and monitor resource usage.

How do I fix 'MCP server not responding' errors?

First, check if the server process is actually running. Then verify network connectivity and ensure the server isn't overloaded with requests. Consider implementing load balancing if needed.

What should I do if I get permission errors?

Check file and directory permissions, ensure you're running with the correct user account, and avoid running servers as root. Use tools like chmod and chown to fix permissions.

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Last updated: September 21, 2025

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