Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important soybean [Glycine max (L.) Merr.] disease in the North Central States. The effect of tillage, crop sequence, and cultivar on SSR incidence and soybean yield was evaluated in a 3‐yr on‐farm study conducted at Janesville, Sharon, and Waunakee, WI. In the study, arranged in a split‐split‐split‐split plot design, main plots were tillage: moldboard (MB), chisel plow (CP), or no‐till (NT); subplots were 1995 crops: corn (Zea mays L.), small grain, or soybean; sub‐subplots were 1996 crops: corn, small grain, or soybean cultivar. Sub‐sub‐subplots were soybean cultivars planted in 1997. In 1997, SSR incidence averaged >40% at Janesville and Waunakee, and <1% at Sharon; and was lowest in NT (P < 0.001) or when the soybean cultivar S19–90 was planted (P < 0.001). Planting corn or oat (Avena sativa L.) the preceding year (1996) reduced SSR incidence in 1997 (P < 0.001). Yield was highest in NT (P < 0.001), in S19–90 (P < 0.001), and following oat (P < 0.001). Sclerotial density was affected by tillage (P < 0.001). Apothecial numbers were greatest in MB and lowest in NT. Because brown stem rot, Phialophora gregata (Allington and Chamberlain) W. Gams, and SSR developed at Janesville, there was a simple linear relationship between yield and SSR incidence (R2 = 0.35, P < 0.01) only at Waunakee. Soybean yields were greatest when S19–90 was planted in NT following corn or oat.