• The application of selenium fertilizer increased most tomato quality variables. • The selenium fertilizer types had effects on tomato quality variables. • The selenium fertilizer concentrations and its application methods had effects on tomato quality variables. • Tomato quality had different responses to selenium fertilizer among tomato varieties. Selenium biofortification is an effective way to improve the tomato fruit quality, however, it is affected by the selenium fertilizer types, selenium fertilizer application methods, selenium fertilizer concentrations, and tomato varieties. We performed 696 pairs of data for meta-analysis using a random-effects model to study the effects of selenium fertilizer application on tomato fruit quality. The results showed that selenium fertilizer application had a significant positive effect on most nutritional quality variables of tomatoes, while there was no change in nitrate content (SMD=−0.557; 95% CI: −2.1∼0.987) and fruit firmness (SMD=0.172; 95% CI: −0.077∼0.422) of tomatoes under application of selenium fertilizer, and similar conclusions were also drawn on nutrients (except for Fe and Ca). For different types of selenium fertilizer, the response of most tomato quality variables to Na 2 SeO 3 was more significant than that to Na 2 SeO 4 . The response of tomato quality variables to selenium fertilizer application methods was different, furthermore, the total soluble solids, sugar-acid ratio, and vitamin C improved the most in soil fertilization, while the concentrations of soluble sugar, titratable acid, and lycopene increased the most in leaf spraying. In terms of selenium concentrations, the concentrations of total soluble solids, vitamin C, and nitrate content increased the most when the concentration was 1∼5 mg·L −1 , while the concentrations of soluble sugar, titratable acid, and lycopene improved the most when the concentration exceeds 5 mg·L −1 . For tomato varieties, the improvement of nutritional quality variables of small fruits was better than that of big fruits. Our meta-analysis comprehensively evaluated the response of tomato quality variables to the application of selenium fertilizer and provided an important guide for higher-quality selenium biofortified tomatoes.