High-voltage functional electrical stimulation (HVFES) training of denervated, degenerated muscle (DDM) increases muscle mass and force output, regenerates muscle fibers and restores muscle ultrastructure. However, the effects of this training on the metabolic capacity of DDM have not been reported. Objective: Describe the effects of a novel HVFES exercise protocol on lean muscle, adipose tissue thickness (ATT), and mitochondrial capacity in DDM. Design: Single subject proof of principle investigation, pre/post-intervention. Methods: This study measured changes in muscle thickness, ATT, and mitochondrial capacity in the DDM of a chronically spinal cord injured (SCI) 33-year-old man before and after 20 months of HVFES training. Muscle thickness and ATT were measured with ultrasound. Mitochondrial capacity, measured as the rate of recovery of muscle oxygen consumption using near-infrared spectroscopy, was the metabolic outcome measure. Results: HVFES increased muscle tissue thickness of the right vastus medialis and lateralis from 1.65 cm (SD 0.26 cm) and 1.25 cm (SD 0.24 cm) at six weeks to 1.94 cm (SD 0.47 cm) and 1.68 cm (SD 0.07 cm) at 20 months, respectively. Mitochondrial capacity increased from no detectable metabolic response at 1.3 months of training to 0.30 min−1 at 14 months, 0.91 at 15 months, and 0.99 min−1 at 20 months. Rates were slower than able-bodied values but within the range observed in paralyzed muscle from complete SCI with intact lower motor neurons (LMN). Limitations/Conclusions: HVFES training restored DDM’s mitochondrial capacity in a case study to levels exceeding paralyzed muscle from untrained, complete SCI with intact LMNs; however, more research is needed to replicate this response and determine if increased mitochondrial capacity results in additional metabolic benefits for patients.