External Javascript

I'm trying to use external Javascript files for some of my scripts, rather than put them directly in the header. The scripts work fine when loaded directly, but I can't seem to figure out how to set up the external scripts properly.

I think I have them linked correctly as the link to the external script shows up in my <head> section when checking the source, and I clicked the link and it was to the proper javascript file.

Unfortunately, the actual scripts do not seem to be loading. I tested it with a simple script and it did not load. Is there a step I'm missing besides creating the external file and linking it in my header.php?

Any help would be much appreciated!