My son often complains of back pain as well.
We got him a new mattress, he had been using his since he was two and 11 years later and he is the size of a man now so it did help. We also had him start doing stretches before he played basketball and before he went to bed. My husband is very tall and has back pain issues as well so we are assuming it might just be from growing and sports.
Some things we looked for-
Does the pain occur after laying down at night or in the morning and then improve while moving during the day?
Does a heating pad help?
Does massaging the area or using icy hot relieve the pain (it did for my son so we figured it was more muscle related than joint or intestinal)
Is there any redness or swelling?
Is the pain always in the same area or does it seem to move around?
I don't know if your son is on Prednisone but when mine was he had pains in his back, ankles, and knees. Once he went off the Pred it went away.
We are still not 100% sure his back pain isn't caused by crohn's but the more people I talk to I find back pain in boys at this age isn't too uncommon. I would try some stretching/ massaging/icy hot etc and see if it starts to help. My son got one of the big work out balls to stretch on and it has slowly gone away.