As Little Snitch consists of multiple parts it is essential to run the Little Snitch Uninstaller to make sure all components are removed from your system. Little Snitch 3.4 or newer automatically starts the uninstaller as soon as you move the Little Snitch Configuration into your trash. For earlier versions please locate the installer in the following path /Library/Little Snitch/Little Snitch Uninstaller.app and start it manually.
The uninstaller lets you choose whether to remove or preserve user specific data (like rules and settings). If you want to remove those items manually, delete the following files and folders (the “~” tilde sign refers to your home folder):
/Library/Application Support/Objective Development/Little Snitch/
~/Library/Application Support/Little Snitch/