Existing literature offers little guidance for therapists who provide core stabilisation exercise (CSE) and proprioceptive neuromuscular facilitation (PNF) training to treat chronic low back pain (CLBP). Studies conducting a head-to-head comparison of CSE and PNF training for CLBP are needed. To compare the effects of CSE and PNF training on pain-related outcomes and trunk muscle activity in CLBP patients. Forty-five CLBP patients, ranging from 18 to 50 years of age, were randomly divided and assigned to either a four-week CSE, four-week PNF training, or control group. Pain-related outcomes, including pain intensity, functional disability and patient satisfaction, as well as superficial and deep trunk muscle activity were assessed before and after the four-week intervention, and at a three-month follow-up. Compared to the control group, those in the CSE and PNF training groups showed significant improvements in all pain-related outcomes after the four-week intervention and at three-month follow-up (P < 0.01). Following the four-week intervention, both CSE and PNF training groups demonstrated significant improvement in deep trunk muscle activity, including the transversus abdominis (TrA) and superficial fibres of lumbar multifidus (LM), compared to the control group (P < 0.05). Four-week CSE and PNF training provided short-term and long-term effects on pain-related outcomes, along with increased deep trunk muscle activity in CLBP patients.