Since 2005, there have been no systematic reviews on the effects of multiple manual therapies, including muscle energy technique (MET), on the hamstrings. Therefore, this systematic review aimed to provide clinical evidence for the effectiveness of the MET on hamstring flexibility. We queried 10 electronic databases (PubMed, EMBASE, The Cochrane Library, KISS, NDSL, KMBASE, KISTI, RISS, Dbpia, and OASIS) up to the end of March 2022. This study only included randomized controlled trials (RCTs) investigating the use of MET for the hamstring. The literature was organized using Endnote. Literature screening and data extraction were conducted by two researchers independently. The methodological quality of the included RCTs was evaluated using the Cochrane risk-of-bias tool 1.0, and the meta-analysis was performed using RevMan 5.4. In total, 949 patients from 19 RCTs were selected according to the inclusion criteria. During active knee extension tests, the efficacy between MET and other manipulations did not significantly differ. For sit and reach tests, MET groups had higher flexibility compared to stretching (MD = 1.69, 95% CI: 0.66 to 2.73, p = 0.001) and no treatment (MD = 2.02, 95% CI: 0.70 to 3.33, p = 0.003) groups. No significant differences were observed in the occurrence of adverse reactions. Overall, we found that MET is more efficacious for improving hamstring flexibility compared to stretching and having no treatment during sit and reach tests because it combines isometric contraction with stretching. Owing to clinical heterogeneity, uncertain risk of bias, and the small number of included studies, further high-quality studies should assess the effectiveness of MET.