You can say it to anyone really! It just carries a sense of them being absent from a place where they usually are, while you are still there, and then you greet them when they return. It's a friendly and polite thing to say.
If that feels too much like you're representing the company, you could just make it more of a personal greeting, like "good to see you again", "it's nice to have you back" etc.
And you wouldn't say welcome back if you've both been away, e.g. over the winter break, because it would be strange for you to say "ah you've returned" when you weren't there yourself!