I remember seeing a post about something like that on a voy.com forum for rectal temperatures.
I do not know if this is the movie you are referring to but this is what was posted on a voy.com forum for rectal temperatures. I haven't seen this movie so I can't help you to see if this what you are referring to. I think this movie is called Misunderstood.
Here is the exact post from that forum:
Does anyone know how to get a DVD copy of the movie from 1984 with Jeane Hackman and the kid from ET. Apparently there is a scene that is quite graphic where the boy gets a rectal temp taken.
I have only seen it on VHS.
The scene in questions is probably the most graphic I have seen in a mainstream movie, but it still has its limits. It is not the kid from ET that gets it up the butt, but the other actor Huckleberry Fox. You do see him with his PJs at his knees as his nurse takes it, but the angle is such that your imagination needs to fill in the gaps.
I understand your interest in wanting to see it but when I first saw it I was not expecting it so imagine my surprise as I watched his nurse pull his PJs down right there on camera. If someone told me about it ahead of time I might have been disappointed when I finally saw it because like I said the angle was bad and for all I know he could of had flesh colored pants on. Still with an active imagination to fill in the gaps I have not heard of or seen a better RT scene in a movie with a boy that age. Baby Boom was a great scene, but the fact that the boy in Misunderstood was older and was crying not to have his temperature taken and it was done in front of the other boy (the actor from ET) made the scene very powerful for me.
If anyone is aware of a better one, I would certainly like to hear about it so I too can start an obsessive search for it.