Like all fruit trees, the dwarf cherry must be pruned carefully during the first three years of life. Pruning when the tree is young promotes a strong framework for the tree to withstand wind and weather and to produce fruit. Once the tree is past the three-year mark, a different pruning strategy for dwarf cherry comes into play—that of pruning the top third of the tree to control height and encourage horizontal spreading of branches, keeping the tree's stature small.
Prune dwarf cherry trees in early spring to promote strong branch growth during the growing season. Mentally divide the tree into thirds and work from the bottom up.
Put on gloves to protect your hands. Clip away shoots and suckers from the bottom third of the trunk with short-handled pruning shears. These shoots will sap energy from the tree and will never produce fruit if you leave them alone, especially in the first three years of the tree's life.
Cut away limbs from the top two-thirds of the dwarf cherry with long-handled pruning shears. Prune branches that cross or rub each other and densely growing branches, leaving six ot seven laterally growing "scaffold" branches springing from a central leader. This will ensure that light and air can penetrate the canopy of the tree, resulting in more fruit and healthier foliage.
Prune for maintenance after the third year. Clip off vertically growing shoots from the top two-thirds of the scaffold branches in early spring and again in fall. These shoots and suckers will crowd the canopy and keep light and air from circulating freely.
Cut the top one-third of the central leader (the tallest branch at the centre of the tree) with long-handled pruning shears to control the height of the dwarf cherry tree and encourage lateral growth of the scaffold branches.
Cut branches and limbs into manageable pieces and discard in yard waste bags.
Pruning of dead and damaged branches can be done at any time of year, as you see them.
Do not do major pruning of cherry trees in summer unless you want to seriously slow the growth of the tree. Avoid pruning in winter because it makes the tree vulnerable to disease from the constant moisture of rain, sleet and snow.