Background: Despite the potential benefits, the effects of Hybrid Assistive Limb (HAL) gait training on changes in neuromuscular activation that accompany functional gains in individuals with spinal muscular atrophy (SMA) type III is not well known. In this article, we quantify the effects of HAL gait training on spatial muscle activity patterns in a patient with SMA type III using multi-channel surface electromyography (SEMG). Methods: A 21-years old male (168 cm, 47.8 kg) with spinal muscular atrophy type III, when diagnosed at 18-years old by genetic screening, participated in this case study. Although he presented with forearm distal muscle weakness, atrophy of the intrinsic muscles of the hand, and neuromuscular fatigue, his activities of daily living is independent. The patient underwent a separate, single 33-minute session of both HAL and treadmill gait training. To evaluate the coefficient of variation (CoV) of force and alterations in the SEMG spatial distribution patterns, modified entropy and CoV of root mean square (RMS) were calculated from the vastus lateralis (VL) muscle before and after the intervention of HAL and treadmill gait training. Each training session was separated by a period of one month to avoid cross-over effects. Results: There was a greater decrease in the ΔCoV of force and an increase in the magnitude of whole VL muscle activation from pre-intervention to post-intervention with the HAL gait training as compared to the treadmill gait training. In response to only HAL gait training, the CoV of RMS was higher, and the modified entropy was lower post-intervention than pre-intervention. Conclusions: Our results support the notion that HAL gait training has a positive benefit on motor output not only in the magnitude of SEMG generated but also the patterns of neural activation.