Aerobic exercise is typically associated with expansion of the mitochondrial protein pool and improvements in muscle oxidative capacity. The impact of aerobic exercise intensity on the synthesis of specific skeletal muscle protein subfractions is not known. We aimed to study the effect of aerobic exercise intensity on rates of myofibrillar (MyoPS) and mitochondrial (MitoPS) protein synthesis over an early (0.5–4.5 h) and late (24–28 h) period during postexercise recovery. Using a within-subject crossover design, eight males (21 ± 1 yr, V̇o2peak 46.7 ± 2.0 ml·kg−1·min−1) performed two work-matched cycle ergometry exercise trials (LOW: 60 min at 30% Wmax; HIGH: 30 min at 60% Wmax) in the fasted state while undergoing a primed constant infusion of l-[ ring-13C6]phenylalanine. Muscle biopsies were obtained at rest and 0.5, 4.5, 24, and 28 h postexercise to determine both the “early” and “late” response of MyoPS and MitoPS and the phosphorylation status of selected proteins within both the Akt/mTOR and MAPK pathways. Over 24–28 h postexercise, MitoPS was significantly greater after the HIGH vs. LOW exercise trial ( P < 0.05). Rates of MyoPS were increased equivalently over 0.5–4.5 h postexercise recovery ( P < 0.05) but remained elevated at 24–28 h postexercise only following the HIGH trial. In conclusion, an acute bout of high- but not low-intensity aerobic exercise in the fasted state resulted in a sustained elevation of both MitoPS and MyoPS at 24–28 h postexercise recovery.