This systematic review aimed to investigate the methodological quality and the effects of fundamental motor skills and physical activity interventions on cognitive and academic skills in 3- to 7-year-old children with special educational needs. The review was reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA 2020) statement. A literature search was carried out in April 2020 (updated in January 2022) using seven electronic databases, including ERIC, Scopus, Web of Science, PsycINFO, CINAHL, PubMed, and SPORTDiscus. The methodological quality of the studies was assessed with Effective Public Health Practice Project (EPHPP) Quality Assessment Tool. Cohen’s d effect sizes and post-hoc power analyses were conducted for the included studies. Altogether 22 studies (1883 children) met the inclusion criteria, representing children at-risk for learning difficulties, due to family background (nstudies = 8), children with learning difficulties (nstudies = 7), learning disabilities (nstudies = 5), and physical disabilities (nstudies = 2). Two of the included 22 studies displayed strong, one moderate, and 19 studies weak methodological quality. The intervention effects appeared to be somewhat dependent on the severity of the learning difficulty; in cognitive and language skills, the effects were largest in children at-risk due to family background, whereas in executive functions the effects were largest in children with learning disabilities. However, due to the vast heterogeneity of the included studies, and a rather low methodological quality, it is challenging to summarize the findings in a generalizable manner. Thus, additional high-quality research is required to determine the effectiveness of the interventions.