The problem is most likely cherry fruit fly (CFF). CFF overwinters in the ground and emerges about the time that the cherries begin to turn from green to yellow (this depends on the variety, but in our area the fly usually emerges in late May. In order to control the insect you must spray the entire tree with a product that contains spinosad every 7 days from late May through harvest. You will need to check the label of insecticide at local garden stores in order to find an insecticide with this product. This product is made from a fungus and is very safe to humans.