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Pruning fruit trees should almost always be done during the winter, or dormant season. This is when the leaves have all fallen and the structure is more easily identifiable. Fruit tree pruning should take place annually, beginning in the first year. There are three stages of pruning that take place during the life of a fruit tree. The three stages are transplant, training, and mature.

Immediately after transplant, fruit tree pruning consists of cutting back nearly all branches, leaving only the trunk a few feet high. This will allow a gardener to train the tree to grow a certain way. The two most common fruit tree pruning orientations are the central leader and the open center. The shape that will work the best depends on the type of fruit tree being grown.

The training stage of pruning fruit trees consists of cutting back certain branches in order to maintain the desired shape. The fruit of the tree should also be thinned out, as this will provide room for larger, healthier fruit. Once mature, the only fruit tree pruning necessary is thinning out of the fruit, and ensuring that all branches and leaves have direct access to sunlight for most of the day.