The age range of 3–6 years is considered as a critical period in developing and learning fundamental motor skills (FMS). To make the formulation of future FMS guidance programs more targeted, we examined gender differences in children’s FMS proficiency using a meta-analysis. Structured electronic databases including PubMed, Scopus and Web of Science were systematically searched using key terms, and the Joanna Briggs Institute (JBI) was used to assess the quality of included literature. Finally, 38 articles (39 studies) met the pre-specified inclusion criteria. The results showed that boys had higher proficiency in total FMS and object control skills than girls (SMD = 0.17 (95% CI 0.03, 0.31), p = 0.02; SMD = 0.48 (95% CI 0.38, 0.58), p < 0.00001), and gender differences in locomotor skill proficiency approached significance, trending in favor of girls (SMD = −0.07 (95 % CI −0.15, 0.01), p = 0.09, I² = 66%). Meta-regression shows that age is associated with gender differences in object control skills (p < 0.05). In addition, through subgroup analysis, we found that boys’ advantage in object control skills increased with age (3 years: SMD = 0.27 (95% CI 0.00, 0.54), p < 0.00001; 4 years: SMD = 0.58 (95% CI 0.38, 0.77), p < 0.00001; 5 years: SMD = 0.59 (95% CI 0.31, 0.88), p < 0.00001; 6 years: SMD = 0.81 (95% CI 0.61, 1.01), p < 0.00001). In this meta-analysis, we found gender differences in FMS levels in children aged 3–6 years. Notably, gender differences in skill proficiency in object control were influenced by age. We recommend focusing on and developing girls’ object control skills starting at age 3.