Maintaining muscle mass and function during rehabilitation from anterior cruciate ligament injury is complicated by the challenge of accurately prescribing daily energy intakes aligned to energy expenditure. Accordingly, we present a 38-week case study characterizing whole body and regional rates of muscle atrophy and hypertrophy (as inferred by assessments of fat-free mass from dual-energy X-ray absorptiometry) in a professional male soccer player from the English Premier League. In addition, in Week 6, we also quantified energy intake (via the remote food photographic method) and energy expenditure using the doubly labeled water method. Mean daily energy intake (CHO: 1.9–3.2, protein: 1.7–3.3, and fat: 1.4–2.7 g/kg) and energy expenditure were 2,765 ± 474 and 3,178 kcal/day, respectively. In accordance with an apparent energy deficit, total body mass decreased by 1.9 kg during Weeks 1–6 where fat-free mass loss in the injured and noninjured limb was 0.9 and 0.6 kg, respectively, yet, trunk fat-free mass increased by 0.7 kg. In Weeks 7–28, the athlete was advised to increase daily CHO intake (4–6 g/kg) to facilitate an increased daily energy intake. Throughout this period, total body mass increased by 3.6 kg (attributable to a 2.9 and 0.7 kg increase in fat free and fat mass, respectively). Our data suggest it may be advantageous to avoid excessive reductions in energy intake during the initial 6–8 weeks post anterior cruciate ligament surgery so as to limit muscle atrophy.