Yes, you can add a custom javascript, or similar script to your website. Scripts, or software such as Live Person, Live Chat, Stats, Website Statistics, Validation, Videos and other services you may want to use on your website may require you to add a javascript or other script to your website header between the <HEAD> </HEAD> tags.
You cannot use server side scripts such as includes, ASP, PHP, etc.
To add a script, do the following:
Login to your website administration.
Click on the Website Settings icon.
Find the section: Custom Header-Footer Script/HTML/Text.
Then in the text box labeled: "Website Header is ran between the <head> tags."
Paste your script or code.
Click "Save Changes" located at the bottom of the webpage.
Note: Anything pasted into this textbox will appear on all your websites pages, not just the home page.