UPDATE: In the later versions global font/size setting under Settings (Preferences) | Appearance also controls the project view tool window font, but there is still no way to control the project view font individually, without changing the font/size of the other UI elements.
Increase the resolution of your monitor in your computer's video card settings. Everything will get smaller. Then you can increase the size of your font in the editor to compensate. Of course, that might make other programs control features seem too small, but if you're saying it is too big, you're probably are using a low resolution (below 1268x1024). Then again maybe you have awesome vision and everything looks big to you because you can see small things really well.
There you can choose the font and the size of everything: menus, Project panel, Editor, etc...
For me, on Linux, it is fine to set it to 15 (default is 14), and then adjust the Editor font alone under:
Editor | General
Mouse
[ ] Change font size (Zoom) with Ctrl+Mouse Wheel
I recently had the problem as well; suddenly the font in the project panel was larger than the others. However, I found a hidden option in the settings of IntelliJ which disables this odd behavior:
Open the file ~\.IdeaIC2018.1\config\options\ide.general.xml
Set the entry with key bigger.font.in.project.view to false
The fix for me was to switch the Theme from GTK+ to IntelliJ, I confirm that Darcula works as well. The fonts broke for me following a switch to proprietary NVIDIA video drivers. On Manjaro Linux running Android Studio.