This pilot study aimed to evaluate the long-term effects of Whole-Body Vibration (WBV) on hind limb muscles, gait and pain in lame dogs with borderline-to-severe hip dysplasia. Ten lame client-owned dogs with borderline-to-severe hip dysplasia, aged from 1.5 to 9.0 years and weighing 14.5 to 53.0 kg, were enrolled. The WBV training program consisted of 15 min sessions three times weekly for 16 weeks. Muscles of the hind limbs were evaluated using measurements of thigh circumference, the cross-sectional thickness of selected hind limb muscles by ultrasound assessment, and vastus lateralis muscle activity determined by surface electromyography (EMG). Lameness and clinical signs of pain were assessed by visual lameness scoring, orthopedic examination and an owner-based questionnaire. Kinetic analysis was performed by using a pressure-sensitive walkway. Manual thigh circumference measurements of both hind limbs showed significant increases over the trial period with a greater degree of change observed after week 8. Ultrasound measurements of the left gluteal muscles and the quadriceps femoris muscles of both hind limbs showed significant increases in the cross-section thickness post WBV. Owner’s perception of pain also showed a decrease in signs of pain at week 12 and week 16 compared to baseline. Based on graphs of the EMG activity patterns of the vastus lateralis muscle, 65% of the hind limbs had an improvement after 48 WBV sessions when compared to pre-session patterns. However, no significant differences were observed in visual lameness evaluation and kinetic analysis. Therefore, further studies will help to better clarify the role of WBV in canine rehabilitation protocols.