window.GlobalVar will be accessible outside of your function.
What's probably going wrong here is that you're trying to access it before it has been set, seeing as it is being set in a callback function.
getCurrentPosition prompts the user for coordinates, but it is not a blocking call, i.e. it does not simply halt all code execution and wait for the user to make a decision.
This means that you do not set window.GlobalVar during page load, you request it during page load, and you set it whenever the user decides to. So no matter where you call getCurrentPosition you cannot be sure that at a given point, window.GlobalVar will be set.
If you want to be sure that window.GlobalVar is set in the script you're running, you need to make sure that you're running the script after the variable has been set.
navigator.geolocation.getCurrentPosition(function(position) {
var gps = (position.coords.latitude+position.coords.longitude);
window.GlobalVar = gps;
continueSomeProcess();
});
function continueSomeProcess() {
// this code will be able to access window.GlobalVar
}