The purpose of this study was to examine changes in motor unit activity in the biceps brachii muscle after an initial ( Bout 1) and repeated ( Bout 2) session of eccentric exercise separated by 1 wk. Eight subjects (aged 22 ± 2 yr) participated in experimental assessments of neuromuscular function obtained before, immediately after, 24 h after, and 7 days after each exercise bout. Each experimental session involved assessments of elbow-flexor force and biceps and triceps brachii electromyography during maximum voluntary isometric contractions (MVCs) and constant-force isometric contractions at five contraction intensities (5–50% MVC), along with indicators of muscle damage (muscle pain and passive tension). In addition, motor unit recordings were obtained before exercise, 7 days after Bout 1, and 24 h after Bout 2 to assess motor unit synchronization and recruitment thresholds. Following a single eccentric exercise session that elicited significant indicators of muscle damage, we found a 57% increase in motor unit synchronization 7 days later compared with before exercise, despite the recovery of maximal strength, soreness, and relaxed elbow-joint angle at this time. Furthermore, a second bout of the same eccentric exercise resulted in reduced indicators of muscle damage and a decline in the strength of motor unit synchronization (24 h after Bout 2) toward levels observed before both exercise sessions. In contrast, no changes in motor unit recruitment thresholds were observed 7 days after Bout 1 or 24 h after Bout 2 compared with before exercise. The increased motor unit synchronization 7 days after a single eccentric exercise session provides new evidence of changes in motor unit activity during the putative repair and regeneration phase following eccentric muscle damage.