Background: this study examined the effects of caffeine supplementation on anaerobic performance, neuromuscular efficiency and upper and lower extremities fatigue in Olympic-level boxers. Methods: Eight male athletes, members of the Spanish National Olympic Team, were enrolled in the study. In a randomized double-blind, placebo-controlled, counterbalanced, crossover design, the athletes completed 2 test sessions after the intake of caffeine (6 mg·kg−1) or placebo. Sessions involved initial measures of lactate, handgrip and countermovement jump (CMJ) performance, followed by a 30-seconds Wingate test, and then final measures of the previous variables. During the sessions, electromiography (EMG) data were recorded on the gluteus maximus, biceps femoris, vastus lateralis, gastrocnemius lateral head and tibialis anterior. Results: caffeine enhanced peak power (6.27%, p < 0.01; Effect Size (ES) = 1.26), mean power (5.21%; p < 0.01; ES = 1.29) and reduced the time needed to reach peak power (−9.91%, p < 0.01; ES = 0.58) in the Wingate test, improved jump height in the CMJ (+2.4 cm, p < 0.01), and improved neuromuscular efficiency at peak power in the vastus lateralis (ES = 1.01) and gluteus maximus (ES = 0.89), and mean power in the vastus lateralis (ES = 0.95) and tibialis anterior (ES = 0.83). Conclusions: in these Olympic-level boxers, caffeine supplementation improved anaerobic performance without affecting EMG activity and fatigue levels in the lower limbs. Further benefits observed were enhanced neuromuscular efficiency in some muscles and improved reaction speed.