School gardening activities (SGA) combined with physical activities (PA) may improve childhood dietary intake and prevent overweight and obesity. This study aims to evaluate the effect of SGA combined with PA on children’s dietary intake and anthropometric outcomes. We searched studies containing randomized controlled trials up to January 2021 in Web of Science, PubMed, Cochrane Library, and the EBSCO database on this topic for children aged 7 to 12 years. Fourteen studies met the requirements for meta-analysis (n = 9187). We found that SGA has no obvious effect on improving children’s BMI (WMD = −0.49; p = 0.085; I² = 86.3%), BMI z-score (WMD = −0.12; p = 0.235; I² = 63.0%), and WC (WMD = −0.98; p = 0.05; I² = 72.9%). SGA can effectively improve children’s FVs (WMD = 0.59, p = 0.003, I² = 95.3%). SGA combined with PA can significantly increase children’s FVs but cannot greatly improve weight status. Although more studies on this topic are needed to prove the effectiveness of this method, the results of our review show that both SGA and SGA combined with PA has a modest but positive impact of reducing BMI and WC outcomes but can significantly increase children’s FVs.