If I'm closing a project and then just delete the project folder, after PyCharm restarts an empty project folder is created again.
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In PyCharm 2018 I finally had to resort to deleting .idea folder and the project went away.
If you want to remove the project from the recent projects list, just highlight the project with your mouse and hit the del key.
In version 2017.2.1
File -> close project
You will be taken to the start up window, where you can see the projects you've created on the left. You can then delete a project by clicking the cross sign('x') following the project name.
This is for PyCharm 2019.1, but I can bet this will work in previous versions.
I am assuming you are in a Unix based operating system (macOs or any Linux distribution). I am also assuming you have currently opened the project you want to remove.
File -> Close Project
The previous command will work in macOS and Linux. In Windows, you can delete it manually by locating the projects directory using File Explorer.
That's it, the project has been completely deleted!