Abstract Background Studies comparing the effectiveness of telerehabilitation and spinal manual therapy (SMT) for chronic non-specific low-back pain (NSLBP) are limited. This study aimed to compare the efficacy of the telerehabilitation-based McKenzie therapy (TBMT) and SMT among patients with NSLBP. Methods Forty-nine consenting patients randomised into either TBMT (n = 28) or SMT (n = 21) group completed the study. TBMT is a mobile phone-based telerehabilitation involving the ‘McKenzie extension protocol’. SMT is a grade II (10 oscillations) posterior-anterior central vertebral pressure on the offending spinous process. Both interventions were applied thrice weekly for eight weeks, and outcomes were assessed on Pain Intensity (PI), Activity Limitation (AL), Participation Restriction (PR), and Health-related Quality of Life (HRQoL) in the fourth and eighth weeks. Results Within-group comparison across baseline, 4th and 8th week indicate that SMT had a significant effect on PI (F = 132.804, p = 0.001), AL (F = 75.984, p = 0.001), PR (F = 99.428, p = 0.001) and for all the scales of SF-12 except for mental health domain (p > 0.05). Similarly, TBMT had a significant effect on PI (F = 243.631; p = 0.001), AL (F = 85.930; p = 0.001), PR (F = 48.425; p = 0.001), and for all the scales except also for mental health domain (p > 0.05). However, there were no significant differences (p > 0.05) in the treatment effects between SMT and TBMT, except for the ‘health perception’ (p = 0.045) scale at week four and the ‘mental health’ scale (p = 0.023) at week eight. Conclusion Telerehabilitation-based McKenzie method and SMT are effective in chronic NSLBP, with TBMT leading to significantly higher long-term health perception improvement. Trial Registration Pan African Clinical Trial Registry (PACTR202010667228786), Registered 27 October 2020-Retrospectively registered.