My little boy had the same problem. It always happened at night, but in his case, his gag reflex really kicked in and he was full-on vomitting. At first I thought he had the flu, but he would be better in the morning. This happened every single night for a week and I took him to the doctor. We described what was happening and the doctor knew exactly what to do. There are many different medications, I am sure, but my son was prescribed Reglan. He took a pill with dinner and again at bedtime. The vomitting stopped immediately. The medicine helps the food to go down further into the digestive tract instead of staying too long in the upper stomach giving the acid a chance to creep back up. My son had no side affects from the medication.
The other things you can do are to try to give your son dinner earlier, (if possible), and get him a wedge pillow or find some other way to elevate him and keep him from sleeping completely flat. The doctor suggested we actually put something under the mattress so that he could sleep on an incline, but the pillows worked fine. Eventually, my son was fine without the medication and only takes it on occasion.
I would suggest definitely taking him to the doctor as acid reflux DOES occur in children and it's best to treat it so that the acid doesn't cause any other problems.
Best of luck to you!