Tomato (Solanum lycopersicum) is a widely consumed vegetable, and the tomato fruit weight is a key yield component. Many quantitative trait loci (QTLs) controlling tomato fruit weight have been identified, and six of them have been fine-mapped and cloned. Here, four loci controlling tomato fruit weight were identified in an F2population through QTL seq.;fruit weight 6.3 (fw6.3) was a major-effect QTL and its percentage of variation explanation (R2) was 0.118. This QTL was fine-mapped to a 62.6 kb interval on chromosome 6. According to the annotated tomato genome (version SL4.0, annotation ITAG4.0), this interval contained seven genes, includingSolyc06g074350(theSELF-PRUNINGgene), which was likely the candidate gene underlying variation in fruit weight. TheSELF-PRUNINGgene contained a single-nucleotide polymorphism that resulted in an amino acid substitution in the protein sequence. The large-fruit allele offw6.3(fw6.3HG) was overdominant to the small-fruit allelefw6.3RG. The soluble solids content was also increased byfw6.3HG. These findings provide valuable information that will aid the cloning of theFW6.3gene and ongoing efforts to breed tomato plants with higher yield and quality via molecular marker-assisted selection.