This study presents a novel compound muscle action potential (CMAP) examination of motor unit changes in paretic muscle post stroke. CMAP scan of the first dorsal interosseous (FDI) muscle was performed bilaterally in 16 chronic stroke subjects. Various parameters were derived from the CMAP scan to examine paretic muscle changes, including CMAP amplitude, D50, step index (STEPIX) and amplitude index (AMPIX). A significant decrease in CMAP amplitude and STEPIX was observed in paretic muscles compared with contralateral muscles (CMAP amplitude: paretic (9.0±0.5) mV, contralateral (11.3±0.9) mV, P=0.024; STEPIX: paretic 101.2±7.6, contralateral 121.9±6.5, P=0.020). No significant difference in D50 and AMPIX was observed between the paretic and contralateral sides (P>0.05). The findings revealed complex paretic muscle changes including motor unit degeneration, muscle fiber denervation, reinnervation and atrophy, providing useful insights to help understand neuromuscular mechanisms associated with weakness and other functional deterioration post stroke. The CMAP scan experimental protocols and the applied processing methods are noninvasive, convenient, and automated, offering practical benefits for clinical application.