Laser acupuncture has been studied extensively over several decades to establish evidence-based clinical practice. This systematic review aims to evaluate the effects of laser acupuncture on pain and functional outcomes when it is used to treat musculoskeletal disorders and to update existing evidence with data from recent randomized controlled trials (RCTs). A computer-based literature search of the databases MEDLINE, AMED, EMBASE, CINAHL, SPORTSDiscus, Cochrane Library, PubMed, Current Contents Connect, Web of Science, and SCOPUS was used to identify RCTs comparing between laser acupuncture and control interventions. A meta-analysis was performed by calculating the standardized mean differences and 95% confidence intervals, to evaluate the effect of laser acupuncture on pain and functional outcomes. Included studies were assessed in terms of their methodological quality and appropriateness of laser parameters. Forty-nine RCTs met the inclusion criteria. Two-thirds (31/49) of these studies reported positive effects, were of high methodological quality, and reported the dosage adequately. Negative or inconclusive studies commonly failed to demonstrate these features. For all diagnostic subgroups, positive effects for both pain and functional outcomes were more consistently seen at long-term follow-up rather than immediately after treatment. Moderate-quality evidence supports the effectiveness of laser acupuncture in managing musculoskeletal pain when applied in an appropriate treatment dosage; however, the positive effects are seen only at long-term follow-up and not immediately after the cessation of treatment.