Use git to clone, then import the project directory as an existing project in IntelliJ IDEA.
Remember to change directories and package names as you require.
Currently only Android and Desktop modules are provided.
The gdx jar files included are not up-to-date. Check out libgdx-updater if you wish to update the libraries.
arobotd/libgdx-intellij-project-skeleton
A newly created libgdx project for IntelliJ IDEA with Desktop and Android modules.
Java