Juniper trees perform best when kept neat, compact and healthy by pruning, but these trees pose a unique challenge for gardeners. The center of the plant stops producing as the plant ages, so the juniper cannot be pruned as severely as other trees and shrubs. The University of Missouri recommends pruning juniper in March or April.
Check your juniper for dead, diseased or damaged branches. Diseased or damaged branches will show scars, cuts, bruising or discoloration. Dead branches won't move with the wind and will feel hollow. This wood needs to be removed for the health of the tree.
Prepare a sanitizing solution by mixing 1-part bleach with 10-parts water in a bucket. Place your pruning tools in the bucket. Then cut off the unhealthy wood at its intersection with the trunk or with a main branch. In between every cut, place the tools back in the sanitizing solution to cleanse.
Trim back the overall size of the plant by shortening long limbs. The University of Missouri recommends pruning juniper branches back to a Y-intersection to promote a more compact juniper.
Cut down the juniper's height by 20 percent if you feel the tree is too tall. Prune back the top branches and outer branches.