The aim of this systematic review and meta-analysis is to evaluate the effectiveness of osteopathic manipulative treatment (OMT) for gastrointestinal disorders in term and preterm infants. Eligible studies were searched on PubMed, Scopus, Embase, Cochrane, Cinahl, and PEDro. Two reviewers independently assessed if the studies were randomized controlled trials (RCTs) and retrospective studies with OMT compared with any kind of control in term or preterm infants to improve gastrointestinal disorders. Nine articles met the eligibility criteria, investigating OMT compared with no intervention, five involving term infants, and the remaining treating preterm infants. Five studies showed low risk of bias. In the meta-analysis, two studies were included to analyze the hours of crying due to infantile colic, showing statistically significant results (ES = −2.46 [−3.05, −1.87]; p < 0.00001). The quality of evidence was “moderate”. The other outcomes, such as time to oral feeding, meconium excretion, weight gain, and sucking, were presented in a qualitative synthesis. OMT was substantially safe, and showed efficacy in some cases, but the conflicting evidence and lack of high-quality replication studies prevent generalization. High-quality RCTs are recommended to produce better-quality evidence.