Version: 10.7.0
Platform: Windows 10 x64
Subsystem: fs

The documentation for fs.rename is not entirely correct or at least incomplete.
It is documented to

Asynchronously rename file at oldPath to the pathname provided as newPath. In the case that newPath already exists, it will be overwritten.

At least on Windows it will also work on directories but it will not overwrite a destination directory but instead throw a EPERM error indicating a permission problem.
If oldPath is a directory and newPath is a file, the file will be replaced, if oldPath is a file and newPath is a directory, the exception is thrown.

Now I'm going to say it's probably a good thing that it's not replace an entire directory but the EPERM error message is misleading and it would probably be better to be precise in the documentation:

Asynchronously rename file or directory at oldPath to the pathname provided as newPath. In the case that newPath is a file and already exists, it will be overwritten, if there is a directory at newPath an error will be raised instead.