Pecan trees are normally pruned for shaping and branch strength during the first five years after planting. Mature trees are pruned to remove dead and diseased wood and to open the center up to allow for sun and air circulation. The more you prune the tree, the longer it will take for the pecan growth, but you will have a much stronger and healthier tree that will produce more pecans over a longer life span. By pruning the tree during its young years, you will have a beautiful, well-shaped tree.
Prune back one third to one half of the whip at planting. A whip is a young tree purchased for planting. The whip should stand about 3 to 3 1/2 feet tall after cutting.
Cut the strongest central leader back by 1/3 of its length during the first winter while the tree is dormant. The central leader will be one of the branches that emerge from the cut of the whip. You will want to choose the strongest and most erect branch. There may be two or three shoots coming from the central branch. Cut the second strongest shoot off completely down to the trunk. Other shoots or branches will grow from the side of the tree. The side shoots should have an inch or two of the tips pruned off after they have reached at least 32 inches long. All of this will encourage a strong upward shoot and a thicker but more organized branching.
Cut the central leader back by 1/3 again the second year while the tree is dormant. A new shoot will probably have come up to compete with the central leader and that should be cut off completely. The side shoots can be tip pruned again, only this year there should be more of them. Choose 6 to 10 side shoots to become a permanent scaffold of branches that have a wide angle from the central leader and are evenly distributed around the tree. Prune the rest of the side branches off at the trunk. Do not completely prune off any side branches under four feet off the ground that are not at least one inch in diameter.
The same pruning should be repeated in years three through five. In the third year, the bottom branches should be pruned to make room to move under the tree when it has matured. The bottom branches may need to be pruned again in years four and five.
Prune mature trees by pruning off branches that are rubbing each other, dead branches and any diseased branches. Dead and diseased branches can be pruned any time of year, but all other pruning should be done in the winter. Thinning out the inside branches will also help let in the sun and air. This will discourage disease and insect invasion into the tree. Any branches pruned at this point should be discarded in the trash or burned to prevent the spread of disease and insects.