Aim: The aim of this study was to assess the pattern of voluntary movements in patients with spinal cord injury (SCI) post intensive whole-body training vs. upper body training with brain motor control assessment (BMCA). Methods: Twelve neurologically intact participants and 18 patients with SCI participated in this study as part of a multi-centre randomised controlled trial. All participants received 12 weeks training (three times per week), which comprised trunk, upper and lower limb exercises and locomotor training and functional electrical stimulation-assisted cycling in whole-body training group and an upper body strength and fitness program for upper body training group. Results: Generalised linear model analysis showed significant effect of the main effect of the Task (P 0.05). Some participants showed significant improvement in muscle strength post 12 weeks training; however, this improvement was not reflected in the pattern of muscle activation which was captured by BMCA. Conclusion: BMCA is a valuable objective assessment tool that could add resolution to the clinical evaluation of patients with SCI post different therapeutic techniques.