1. Back up the database
2. Run the installer; the recent installers (5.6+) can upgrade reasonably well. Otherwise, download the latest version.
3. Run mysql_upgrade and restart MySQL. See http://dev.mysql.com/doc/refman/5.7/en/mysql-upgrade.html

Earlier versions

If version 5.0 is installed, upgrading requires several manual steps. After backing up (exporting) the database:

• Stop the MySQL service
  • Go to services (search from the start menu)
  • Find MySQL, select Stop (right-click)
• Delete the MySQL service
  • Open a Command Prompt in Administrator mode (search for Commadn Prompt, right-click over it, select Ran as administrator)
  • type sc delete MySQL
• Uninstall all MySQL software
  • Go to Control Panel, Programs
  • Uninstall MySQL Administrator, MySQL Tools,, Connectors, and finally MySQL server
• Delete the User files:
  • Navigate to C:\Users\[username]\AppData\Roaming (the "AppData" folder is hidden so you need to type it)
  • Delete the MySQL folder
• Delete remaining files under C:\Program Files and C:\Program Files (x86)

Now you can install a fresh copy of MySQL, and import the saved database.