When And How To Prune an Apple or Pear Tree
Below are some helpful instructions for pruning apple and pear trees, which require the same pruning method. 

Central Leader Method

My preferred method for pruning and training apple and pear trees is the Central Leader Method. A tree pruned using this method takes on the shape of a Christmas tree. Pruned to this shape, the tree will receive the most amount of sunlight to all parts of the tree, resulting in a taller tree that will produce the greatest amount of fruit.

The purpose of pruning a young tree using the central leader method is to control its shape by developing a strong, well-balanced framework of scaffold (main) branches. Unwanted branches should be removed or cut back early to avoid the necessity of large cuts in later years.

Pruning Instructions

Pruning should be done in late winter when the tree is dormant and without foliage.

Newly Planted Young Trees

NOTE: These instructions for "newly planted young trees" do not apply to larger container-grown trees that have been properly pruned by a professional at the nursery where they were grown. If your container-grown apple or pear tree looks similar to the "1st Year" example in the diagram further below, wait to prune until the first dormant season after planting

Newly planted, dormant, bare root or undeveloped container trees should be cut back to 30 to 32 inches at planting time. Do not cut them back if the leaves have already emerged. Wait until late winter in the next dormant season. When you cut the tree back to 30 to 32 inches in height it helps to bring the top into balance, stimulates quick root development, and causes the buds just below the cut to grow and form what will be the main scaffold branches that will be the canopy of your tree over the long term. If you cut the tree off too low, at 24 inches, this will result in excessive vegetative growth. Cutting too high, at 36 inches, will result in weak growth in the top of the tree as well as in lower areas of the tree.

After having cut the new tree back to 30-32 inches, and a few weeks after new growth begins to develop, the buds below where you made your cut should be sending out shoots that will develop into branches. Plan to keep 5 or 6 of these developing shoots as the main branches of your tree. Select ones that are equally spaced around the trunk and which are arranged vertically on the trunk at 4 to 10 inches above or below each other. 

These vigorous shoots are often upright growing, sometimes too upright. To develop a more open tree and balanced tree that will support itself, it's a good idea to force the new shoots to a more horizontal growth pattern at an angle of 45 to 60 degrees, as shown in the diagram above. To accomplish this, when the new shoots have grown to 2 to 3 inches in length you can position wooden spring-type clothespins, or some other form of brace, between the main trunk or branch and the new shoot, as shown in the diagram above. Allow the most vigorous upright branch at the highest point on the trunk to remain growing straight up as this will become the central leader of your tree. 

NOTE:  It is important that the limbs are spread when they are young. If a limb is not spread a bark inclusion can develop. This occurs when the bark of the trunk and the branch have been pressed together. This structure weakens the branch and serves as an entry point for pathogens. The wide-angled branch, however, allows for growth and expansion of both the trunk and the branch and produces a much stronger branch that can withstand future loads of heavy fruit.

First Year, or Second Year for Bare Root

After having pruned your young, newly planted apple or pear tree, the 4 to 6 main branches should have developed after the first growing season. Your objective is to develop the central leader and the main scaffold branches. In late winter, before new growth begins, remove any broken limbs or limbs growing vertically. If the first set of main branches have begun to grow too upright use wooden spreaders, weights, or string to bring them back to a 45 to 60 degree angle.

Optional: Prune the central leader about one-third the length that it grew the first year. Several new shoots should develop just below the cut you made on the central leader. 

Second Year

During the second winter, develop a second set of branches from shoots that have developed on the central leader about 24 inches above the branches you established to begin with. Be sure to clothespin these new shoots to develop wide crotch angles. Remove any other undesirable shoots that are too vigorous or in competition with the central leader during the growing season.

Third Year

Before pruning in the third year or years thereafter, keep in mind that "this year’s growth will carry next year’s fruit." So, when you’re pruning apple or pear trees, don’t cut off all the new growth because the fruit blossoms will form on the new budding twigs.

When pruning in late winter, start by removing any suckers: the shoots that might have grown up from around the base of the tree. 

Then cut out all the dead branches. If you have a struggling apple tree, you’ll want to prune it when the leaves start growing. This is because it’s easier to see which limbs are dead and which ones are alive. You can and should prune dead or diseased limbs out of the tree at any time during the year.

Then prune out any of the shoots that grew vertically from your main scaffold branches. These branches don’t produce fruit, don’t support the shape of the tree, and use nutrients that could be used for fruit production.

Then prune out branches that are growing toward the ground. They’re going the wrong direction.

Then remove crossing branches. When you have two branches that are crossing over each other, keep the one that best supports the shape of the tree.

Then reduce the length of the new shoot growth you will keep to 1/4 it's length.

Again, the main objective is to have 4 to 6 main scaffold branches spaced around the tree and then a second set of branches above these. Always make sure that the ends of the scaffold branches are below the end of the central leader after they have been pruned back.

At maturity the overall appearance of the tree should be a pyramid with the largest and longest branches in the lowest and first set of scaffolds followed by 2 to 3 additional sets that are progressively smaller in diameter and shorter in length.

Fourth Year

In late winter, continue to cut off one-quarter the length of newest limbs that grew the previous season, and remove any upright-growing limbs. Any broken or diseased limbs also should be removed. Always maintain the central leader as the highest point on the tree. The ends of the primary and secondary sets of branches should be kept below the top of the tree. Keep the leader dominant by shortening competing branches. Remove branches that form narrow crotch angles and remove weak, twiggy growth.

Fifth Year and Thereafter

During the fifth year, when the tree should begin to bear fruit, discontinue cutting back the newest limbs. At this point, pruning for the rest of the life of the tree will be done to maintain the conical shape. Prune the trees every year in late winter. When pruning, continue to remove upright or downward-growing shoots as they emerge. Try to retain only shoots that are at the 45 to 60 degree angle. Periodically thin out the branching structure to allow adequate light to penetrate the interior and lower portions of the tree.

Keep in mind to always maintain the central leader as the highest point on the tree. The ends of the primary and secondary sets of branches should be kept below the top of the tree.

Rejuvenation Pruning

Many people will purchase a home and property with an old and neglected apple or pear tree growing on it. The previous owners did not take time to properly prune and care for the tree and now it has become overly bushy and weak, and produces few if any apples. Such a tree requires extensive corrective pruning.

The main objective in pruning an old, neglected apple or pear tree is to try to open up the interior to allow good light penetration.

Corrective pruning should be done in late winter, before new spring growth begins to emerge.

As with younger trees, it is necessary to select 4 to 8 lower and upper main scaffold branches with good crotch angles and that are spaced around the tree. Limbs with poor angles, and excess scaffold limbs, should be removed at their base with a pruning saw. Becare not to saw into the main trunk of the tree when removing a large branch/limb. Then remove all the upright or downward growing shoots from the main branches. Cut them off at their base. In some cases it is advisable to spread the corrective pruning over two to three seasons.

When this type of severe pruning is done in the winter the trees should not be fertilized that spring.