Rotating non-host crops for 2-3 years at a time will reduce sclerotia levels in soil. Tillage can be effective, but overall evidence for effectiveness is inconclusive. No-till fields are thought to be more susceptible to disease. Weeds can be hosts for this pathogen, so it's important to minimize weed populations in and around soybean fields. Other measures taken have been increasing row spacing, decreasing number of plants per acre, and planting later in the spring.
Fungicides currently on the market do not offer complete control over sclerotinia stem rot, but they do maintain partial control. They are best used in combination with mechanical and/or cultural control measures. Active ingredients listed for compression and/or control are thiophanate methyl, boscalid, tetraconazole, and prothioconazole. Chemical applied at R1 growth stage has proven more effective than R3. Please contact your local plant pathologist to learn what is most effective in your area and how to use it best. Always read and follow all label instructions.
Though there may not be totally resistant varieties available, be sure to select varieties that do have some resistance to sclerotinia stem rot. Planting cover crops will also provide the potential for seedlings to emerge sooner, thus be less susceptible to infection (earlier flowering). There are certain biological control measures that can be taken. Please contact your local plant pathologist for proper recommendations.