IntroductionAtypical antipsychotics have been studied to treat autism spectrum disorder (ASD). However, like little is known about whether these drugs are effective and safe when compared in controlled and non-controlled settings. This study aims to assess the efficacy and safety of second-generation antipsychotics in ASD in randomised controlled trials (RCT) and observational studies.Methods and analysisThis systematic review will include RCT and prospective cohorts evaluating second-generation antipsychotics in people 5 years and older diagnosed with ASD. Searches will be conducted in Medline, Embase, Cochrane Library, Epistemonikos, Lilacs, CINAHL, PsycINFO, trial registries and grey literature databases without restriction on publication status, year of publication and language. The primary outcomes will be symptoms of aggressive behaviour, quality of life for the individual or their careers, and discontinuation or dropouts/withdrawals of antipsychotics due to adverse events. The secondary outcomes are other not serious adverse events and adherence to pharmacotherapy. Selection, data extraction, and quality assessment will be performed by pairs of reviewers, independently. The Risk of Bias 2 (RoB 2) and Risk of Bias in Non-Randomised Studies of Interventions (ROBINS-I) tools will be used to assess the risk of bias in the included studies. If appropriate, a meta-analysis and network meta-analysis will be conducted to synthesise the results. The overall quality of the evidence for each outcome will be determined by the Recommendation, Assessment, Development and Evaluation approach.Ethics and disseminationThis study will systematically summarise the existing evidence evaluating the use of second-generation antipsychotics for treating ASD, in controlled and uncontrolled studies. The results of this review will be disseminated through peer-reviewed publications and conference presentations.PROSPERO registration numberCRD42022353795.