Dear L.:
Have him drink a lot. Water and fruit juices are best, milk is good but does not 'count' towards drinking. Fruits like prunes, plums, pears and peaches are good.
Check the age and get a stool softener. My son is older and uses Kaopectate, but they may have something for 3-year-olds, too.
Also try prune extract pills (natural and gentle).
Fiber is always good, but only when he drinks enough, otherwise it aggravates the problem.
You can also get probiotics (natural) like acodophilus (not sure about the spelling) and Culurelle (only from Walgreen). Again, check the age.
Finally, look into milk of magnesia (they have cherry-flavored).
Whatever you do, pause after a while so he does not get used to it, or the effect will wear off. Only drinking and fruit should be kept up ongoing. Of course, healthy exercise and play is necessary still.
Good luck,
W.