: Gastrointestinal (GI) symptoms, often reported by individuals with autism spectrum disorders (ASD), may impair functionality and exacerbate behavioral symptoms. Gut dysbiosis has been identified as a potential environmental factor influencing these symptoms through gut-brain axis dysregulation. Fecal microbiota transplantation (FMT) is a promising therapeutic strategy with potential to alleviate symptoms. This review systematically evaluates the efficacy and safety of FMT in GI and ASD-related symptoms. : This systematic review followed PRISMA 2020 guidelines and was registered in PROSPERO. The review included clinical trials on FMT in children and adolescents with ASD, published up to October 2024. The bias assessments were performed using Cochrane tools. Outcomes focused on changes in GI and ASD-related symptoms using scales selected by the authors. : This systematic review included two RCTs and seven before-and-after studies. Improvements in GI and ASD-related outcomes were reported in all before-and-after studies, whereas the results of RCTs were inconsistent. The before-and-after studies showed a high risk of bias, while the RCTs demonstrated a low risk. : Although many studies have been conducted, the methodological limitations of some and contradictory findings of others make it difficult to draw clear conclusions about the effectiveness of FMT in children with ASD. Variations in intervention protocols underscore the importance of establishing standardized FMT procedures in future rigorously designed trials.