My daughter was scared of the " bad guy with scary teeth" in our master bathroom. IDK what she was talking about she was only two. I explained no one was in there and she wasnt having it. I asked my husband to tell the bad man he could not stay in our house and he was not welcome. he had to go outside and could not come back. Several months later she tried to say he was in our bathroom and reminded her that he couldnt come in that daddy said he had to stay outside. She agreed that he was outside and no long inside.
Btw - I dont think your son is actualy scared of a "ghost" but the stories. Meaning the kids could have told stories about "big foot" or a "lumber jack killer" and he would be telling you to sit in the bathroom because of " big foot" or making u look in his room for the "lumber jack killer". Facing your fears might also help. But you know what he can handle and if it will shock him or not.
My son is big into pep talks. Like if it were him I would say things like " your the bravest warrior in the world. you must face this fear and tackle it" your stronger than any silly story" " now go in your room and tell those silly stories to stop messing with you that you arent scared".
I would say these things very dramatic and effective.
For the record - I believe in the afterlife, deamons and perhaps a scientific energy that we call "ghosts" now but I am waiting for science to accept spirts and configure what "orbs" and "transparent ghosts" really are.