Genetic analysis of seed yield is important in the breeding of high-yielding cultivars in soybean (Glycine max (L.) Merr.). Generally, the number of quantitative trait loci (QTLs) associated with seed yield, even in a single population, is high, and thus, the effect of each QTL is small. Lodging tolerance is an important trait that affects yield because soybean plants with higher aboveground weights are easily lodged. We previously identified eight QTLs associated with seed yield and a QTL associated with lodging tolerance, qLS19-1, by using a recombinant inbred line (RIL) population derived from a cross between Japanese cultivars Toyoharuka and Toyomusume. There were significant positive correlations over 3 years between seed yield and the number of favourable alleles at QTLs associated with seed yield in the RILs. The aim of this study was to develop high-yielding lines by using marker-assisted selection for seed yield and lodging tolerance. Six pyramiding lines with favourable alleles at seven QTLs associated with seed yield and qLS19-1 were developed from a cross between two RILs in the same population. The seed yields of six pyramiding lines tended to be greater than those of Toyoharuka (114–124%) and Toyomusume (108–117%) in a 2-year yield trial. Four of the six pyramiding lines produced significantly higher yields and were later maturing than both Toyoharuka and Toyomusume. Our results suggest that marker-assisted selection for seed yield and lodging tolerance in the same population will be effective for high-yield breeding.