As far as I know:- In the sense that both are terms of congratulation or encouragement, there is no difference in meaning; except that "well done" is perhaps more formal than "good job". Both can be said by a parent to a child, by teacher to student, by worker to co-worker, by boss to employee, by your friend to you. Note that "good job" and "well done" have other meanings in different contexts.

So when use "good job" and when use "well done"

good Job is usually a boss's praise.