ABSTRACT Background Transcutaneous electrical spinal cord stimulation combined with activity‐based therapy (TESCS‐ABT) holds promising potential for motor rehabilitation of spinal cord injury (SCI). However, its effectiveness in individuals with chronic complete SCI remains largely unexplored, despite recent evidence suggesting that many of these individuals exhibit signs of neurological incompleteness. This study was a prospective, single‐arm, open‐label trial that investigated the neurophysiological effects of TESCS‐ABT in chronic complete SCI and assessed whether any changes translate into functional improvements. Methods Nine participants with chronic complete SCI were recruited for a two‐phase trial, including 6 weeks of FES‐conditioning and 16 weeks of TESCS‐ABT. Neurophysiological, neurological and functional assessments were conducted at six timepoints throughout the study: baseline; after the FES‐conditioning phase; after 6, 10, and 16 weeks of TESCS‐ABT; and 12 weeks after completion of the intervention. Results All participants exhibited increases in synchronized neural signals to muscles in high frequency bands, with limited improvements in corticospinal and spinal excitability. The magnitude and consistency of these neurophysiological changes varied among participants and were influenced by limb dominance. Neurophysiological improvements did not consistently translate into meaningful gains in strength or function. Conclusions These findings suggest that the neurophysiological effects of TESCS‐ABT depend on the presence of residual supraspinal connectivity in chronic complete SCI. This SCI population demonstrate a more limited response compared to previous reports in individuals with incomplete SCI. This study provides important insights into the mechanisms and potential limitations of TESCS‐ABT, helping to guide future research toward optimizing the therapy and identifying those most likely to benefit. Trial Registration ClinicalTrials.gov identifier: NCT05522920