Capacitive and resistive electric transfer (CRET) therapy is used to reduce pain and improve functional disability, and the effect on low back pain remains to be investigated. This study aimed to examine the immediate effect on the onset time of the muscles after irradiating CRET therapy for non-specific chronic low back pain (NSCLBP). Thirty patients with NSCLBP were randomly divided into an intervention group (n = 15) and a sham group (n = 15). Participants and statisticians were blinded to participant allocation. The intervention group received one 15-minute session of CRET therapy on their lower back; the sham group similarly received one 15-minute session of sham therapy. Before and immediately after the intervention, the onset time of the trunk and lower limb muscles was measured during prone hip extension, and pain intensity was recorded using a visual analog scale. The intervention group showed a significant reduction in pain and a significantly earlier onset time of the thoracic part of the iliocostalis lumborum, lumbar part of the iliocostalis lumborum, lumbar multifidus, and gluteus maximus. These results showed that CRET therapy not only reduced pain, but also facilitated trunk muscle activity. Improvement in muscle activity patterns may improve activities of daily living. This study was registered at the University Hospital Medical Information Network in Japan (UMIN-CTR: 000046301).