Wait to prune your juniper until after its new growth emerges in early spring. Don work gloves, and clean the blades of your pruning loppers and hand pruners with a household antiseptic cleaner. Wipe the blades dry with paper towel. Disinfecting the blades reduces the chance of spreading fungi and diseases among plants.
Examine your juniper, and remove each branch that is dead from its tip to its base. Cut out the dead wood with pruning loppers, cutting each branch just above where it meets the trunk. A juniper tends to die back at its bottom. All juniper branches can die in the center of the shrub when light can't get through dense outer growth.
Cut back overlong branches and those that look unattractive or are partially dead. Make each cut about 1/4 inch above an outward-facing green shoot. Cut at an upward-slanting 45-degree angle, using either the pruning loppers or hand pruners. Remove as much or as little of each branch as you like, as long as you leave on the juniper at least the last green shoot closest to the trunk.
Trim back individual new shoots by one-half their length, cutting 1/4 inch above a shoot growing in the direction in which you want to encourage next spring's growth. Using that technique encourages full growth.