According to their FAQ, GIT doesn't track empty directories.
Git FAQ
However, there are workarounds based on your needs and your project requirements.
Basically if you want to track an empty directory you can place a .gitkeep
file in there. The file can be blank and it will just work. This is Gits way of tracking an empty directory.
Another option is to provide documentation for the directory. You can just add a readme file in it describing its expected usage. Git will track the folder because it has a file in it and you have now provided documentation to you and/or whoever else might be using the source code.
If you are building a web app you may find it useful to just add an index.html file which may contain a permission denied message if the folder is only accessible through the app. Codeigniter does this with all their directories.