The impact of the management variables soybean cultivar, row spacing, population density, and shading was evaluated on the incidence of Sclerotinia stem rot (SSR) on glyphosate-resistant soybeans in an irrigated glyphosate-resistant soybean management system. Soybean canopy development, flower number, soil moisture, disease severity, and soybean yield were evaluated on three glyphosate-resistant cultivars, Pioneer ‘92B71’ (upright), Asgrow ‘AG2701’ (bushy), and Asgrow ‘AG2702’ (bushy). Three different row spacing–target population combinations of 76 cm, 430,000 seeds/ha; 19 cm, 430,000 seeds/ha; and 19 cm, 560,000 seeds/ha were evaluated. Cultivars 92B71 and AG2701 had 42 and 15% lower disease severity indexes and 38 and 19% greater yields than AG2702, respectively. The actual average population of 92B71 was 9 and 20% lower than actual average populations of AG2701 and AG2702, respectively. Disease severity indexes were lower and yield was higher when population was reduced from 560,000 seeds/ha to 430,000 seeds/ha in 19-cm rows. When averaged over the entire study, population was positively correlated with disease severity index (r2 = 0.33; P < 0.0001) and negatively correlated with yield (r2 = −0.13; P = 0.0140). Reduction of soybean population was more important than increasing row spacing to manage SSR in an irrigated system. Average actual spacing between plants within a row was 18 and 4 cm for 19- and 76-cm rows, respectively, at a target population of 430,000 seeds/ha, which may have contributed to greater plant-to-plant transfer of the Sclerotinia sclerotiorum pathogen in the 76-cm rows.