For Windows 7 and Vista users, you will almost certainly need to start Notepad++ as administrator in order to update from Plugin Manager 0.9.3.1 (the version bundled with Notepad++ since about 5.6)
Simply right click the Notepad++ program in your start menu, and click "Run as administrator"
In Notepad++, go to the Plugins menu and choose Plugin Manager, Show Plugin Manager. On the updates tab you'll see Plugin Manager listed and ticked. Just click "Update"
Restart when it asks you to, and then you have the new version.
If you receive a message about GPUP.EXE not being the right version, simply reinstall plugin manager, you won't need to run Notepad++ as administrator to do that.
To help the search engines, the exact message is "The external plugin updater (gpup.exe) under the updater directory does not appear to be the correct version. It will most likely work, but you should reinstall the plugin manager at your next opportunity to ensure full functionality. We'll attempt to use the current version for this operation."
Plugins, Plugin Manager, Show Plugin Manager, go to the "installed" tab, and select Plugin Manager, then click reinstall.
On Windows 7 and Vista, you'll likely get 2 UAC prompts (asking to confirm to perform the action as an administrator), that's completely normal, and has to do with the fact that the GPUP.EXE file needs to be replaced as administrator, and then the new version run to replace the plugin DLL.