//load external js file into header after 2 seconds
setTimeout(function() {
    var headerEl = document.getElementsByTagName("head")[0];   
    var scriptEl = document.createElement('script');
        scriptEl.type = 'text/javascript';
        scriptEl.src = 'http:/www.mywebsite.com/myscript.js';
        headerEl.appendChild(scriptEl);
}, 2000);