The timer will try to execute once your current thread is done. This depends on where you call the window.setTimeout(). If it is in a javascript tag, but not inside a function, then it will be called once the end of the javascript tag is reached. For example:
<html>
<script type="text/javascript">
setTimeout(function(){alert("hello")},0);
var d=Number(new Date())+1000;
while(Number(new Date())<d){
}
alert("hi");
</script>
</html>
If you call the setTimeout inside a function that results from an event occuring, for example onload, then it will wait until the event handler function returns:
<html>
<script type="text/javascript">
document.addEventListener("mousedown",function(){
setTimeout(function(){alert("hello")},0);
var d=Number(new Date())+1000;
while(Number(new Date())<d){
}
alert("hi");
}, true);
</script>
</html>
It is impossible to make one thread in JavaScript wait while another thread is running. Event listeners will wait until the current thread is done before they start running.
The only exception is Web Workers, but they run in a different file, and the only way to communicate between them is using event listeners, so while you can send a message while the other is working, it won't receive that message until it is done, or it manually checks for messages.