After spinal cord injury (SCI), widespread reorganization occurs within spinal reflex systems. Regular muscle activity may influence reorganization of spinal circuitry after SCI. The purpose of this study is to investigate the effects of long-term soleus training on H-reflex depression in humans after SCI. Seven subjects with acute (<7 weeks) SCI (AC group) underwent testing of H-reflex depression at several frequencies of repetitive stimulation. Eight subjects (including 3 from AC) stimulated one soleus muscle daily, leaving the other leg as an untrained within-subject control. Trained limb H-reflexes were assessed during year 1 (TR1) and year 2 (TR2) of training. Untrained limbs were tested during year 2 (UN). H-reflex amplitude was lower at 1, 2 and 5 Hz than at 0.1 or 0.2 Hz (p < 0.05). The pattern of depression differed between AC and UN (p < 0.05), but not between TR2 and UN (p > 0.05) despite significant adaptations in torque and fatigue resistance (p < 0.05). Three subjects who began training very early after SCI retained H-reflex post activation depression, suggesting that early intervention of daily muscular activity may be important.