Some hosts don't allow it. But no, generally you can run most javascript on most websites with nothing special added. A javascript is like a css file or an image file. It's a resource for the page. As long as it's on the server and referenced by its path (if any) and filename with the correct tag, it's available to the page. It's really more like a css file than an image, in that css code can go on the page or in a separate file. So can javascript. The syntax is just a little different.
Many people get excited about javascript when they haven't used it before. Most of it's nothing special. It's just text code that tells the browser what to do, like HTML or css, except that it can do more things in real time in response to the user or other circumstances in ways those others cannot.
There are some security issues with javascript that those other languages don't have. But modern browsers take care of that for you, not allowing anything dangerous or even suspect, erring on the side of caution.
It would probably be a good idea to post a link to your page with the script. That way we could have a better chance to see what's what.
Please post a link to a page on your site that contains the problematic code so we can check it out.
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