Whole-body vibration has been considered as a countermeasure against muscle atrophy. However, its effects on muscle atrophy are poorly understood. We evaluated the effects of whole-body vibration on denervated skeletal muscle atrophy. Whole-body vibration was performed on rats from Day 15 to 28 after denervation injury. Motor performance was evaluated using an inclined-plane test. Compound muscle action potentials of the tibial nerve were examined. Muscle wet weight and muscle fiber cross-sectional area were measured. Myosin heavy chain isoforms were analyzed in both muscle homogenates and single myofibers. Whole-body vibration resulted in a significantly decreased inclination angle and muscle weight, but not muscle fiber cross-sectional area of fast-twitch gastrocnemius compared to denervation only. In denervated gastrocnemius, a fast-to-slow shift was observed in myosin heavy chain isoform composition following whole-body vibration. There were no significant changes in muscle weight, muscle fiber cross-sectional area, and myosin heavy chain isoform composition in denervated slow-twitch soleus. These results imply that whole-body vibration does not promote recovery of denervation-induced muscle atrophy.