Ankle clonus is common after spinal cord injury (SCI) and is attributed to loss of supraspinally mediated inhibition of soleus stretch reflexes and maladaptive reorganization of spinal reflex pathways. The maladaptive reorganization underlying ankle clonus is associated with other abnormalities, such as coactivation and reciprocal facilitation of tibialis anterior (TA) and soleus (SOL), which contribute to impaired walking ability in individuals with motor-incomplete SCI. Operant conditioning can increase muscle activation and decrease stretch reflexes in individuals with SCI. We compared two operant conditioning-based interventions in individuals with ankle clonus and impaired walking ability due to SCI. Training included either voluntary TA activation (TA↑) to enhance supraspinal drive or SOL H-reflex suppression (SOL↓) to modulate reflex pathways at the spinal cord level. We measured clonus duration, plantar flexor reflex threshold angle, timed toe tapping, dorsiflexion (DF) active range of motion, lower extremity motor scores (LEMS), walking foot clearance, speed and distance, SOL H-reflex amplitude modulation as an index of reciprocal inhibition, presynaptic inhibition, low-frequency depression, and SOL-to-TA clonus coactivation ratio. TA↑ decreased plantar flexor reflex threshold angle (-4.33°) and DF active range-of-motion angle (-4.32°) and increased LEMS of DF (+0.8 points), total LEMS of the training leg (+2.2 points), and nontraining leg (+0.8 points), and increased walking foot clearance (+ 4.8 mm) and distance (+12.09 m). SOL↓ decreased SOL-to-TA coactivation ratio (-0.21), increased nontraining leg LEMS (+1.8 points), walking speed (+0.02 m/s), and distance (+6.25 m). In sum, we found increased voluntary control associated with TA↑ outcomes and decreased reflex excitability associated with SOL↓ outcomes.