Japanese cherry trees can grow very large, depending on the variety. Limiting the size of your tree is not difficult. The best time for pruning will depend on the age of the tree. Prune young trees that have not yet filled out completely in the late winter. Established trees that have filled out to your satisfaction, pruning in the summer will inhibit overall growth. By inhibiting height and growth on one side, you can create beautiful sweeping shapes with your Japanese cherry tree.
Top the tree by trimming the vertical growth tips in the winter either with sharp pruning shears or a pruning saw. To top the tree, find a bud at about the height to which you would like to limit the tree's growth. Place the shears about 1/8 to 1/4 inch above the bud and cut the top of the tree off. The angle of the cut should be at least 45 degrees to prevent water from collecting on the cut and potentially introducing disease to the tree.
Topping the tree will prevent the tree from getting taller and encourage more horizontal growth. For taller trees, you may need a ladder to reach the tips that need pruning.
Trim the ends of any branches where you would like to control horizontal growth. Find a bud that is near the maximum desired length for the branch. Make an angled cut between an eighth and a quarter inch from the bud toward the tip of the branch. The angle should be around 45 degrees. If you are using hand pruners that have the cutting blade on top, place the cutting blade on the top of the branch. This should also be done in the late winter to encourage growth in other areas.
Prune dead branches by cutting them off at the trunk. Cut the dead branch about an eighth of an inch above where it joins the trunk. This joint is called the branch collar. For smaller branches, use pruning shears. For larger dead branches, use a fine toothed saw. If you are using hand shears with only an upper cutting blade, place the cutting blade on the top of the branch to be cut. If you are using a saw, saw from the top of the branch down.
If sawing, be sure to support the branch until the cut is completely through the branch to prevent splintering. This will both encourage new, healthy growth and and keep the tree healthy.