var runJavascript:URLRequest = new URLRequest("javascript:javascriptFunction()");
navigateToURL(runJavascript, "_top");

Short and sweet, add the following two lines where you want to trigger a javascript function. Just change the javascript denoted in the code by "javascriptFunction()" with whatever you want to call. Also jsut in case make sure you have the allowScriptAccess parameter set to "always".

Trigger Javascript from Flash with AS3

javascript, actionscript, function

ActionScript 3