Begin pruning a young apple tree the day it is planted. This is to encourage a scaffolding form so sunlight can reach the inside branches and air can circulate around the fruit and leaves, preventing disease and maximizing quality fruit production. This method is called the strong central leader system and is one way to prune apple trees. It creates a cone-shaped tree that is tall but keeps a good shape over the life of the tree, making the tree less prone to wind damage.
How to Prune Young Apple Trees
Cut the one-year old tree or whip to 30 inches from the ground just above a leaf bud. This decreases the demand on the roots of the young apple tree to provide water and nutrients to the new tree until it can get established.
Find new growth on a two-year old tree to make the right cuts for the strong central leader system. Leave the new leader that is forming below the previous cut and growing straight up. Look at the top 10 inches of the main trunk for four new branches growing in four different directions that have wide crotch angles. They probably are not growing at the exact same level, but should be fairly close. Sometimes there are only two or three branches, and you will have to wait for the others to appear at a slightly different level. Cut all other growth off the trunk of the young apple tree except for the scaffolding branches and the leader. Then, cut the central leader by half just above a bud and the scaffolding branches by one-fourth.
Locate new scaffolding branches along the new leader on a three-year old tree and cut them back by one-fourth. The new scaffolding branches should be about 30 inches above, but not directly above, the previous scaffolding branches where they can create shade on last year's growth. You will also see that there are new branches growing at the end of the scaffolding branches trimmed back by one-fourth the previous season. Cut all growth off the end of previous year's scaffold branches except for the one branch that is in the best position, for example growing upward, and cut that one back by one-fourth. Repeat on other previous year's scaffold branches. Then, cut central leader back by one-half just above a bud.
Repeat this procedure every year until there are four sets of scaffold branches 30 inches apart and decreasing in length as they go up the tree. The tree should have a pyramidal shape when it matures.