Blackleg is a major fungal disease of canola caused by Leptosphaeria maculans. Due to the breakdown of current host resistance, having an effective fungicide to avoid seedling infection is important to avoid disease. Pydiflumetofen is a newly developed broad‐spectrum seed treatment fungicide in the succinate dehydrogenase inhibitor (SDHI) group. We evaluated the separate and combined application of pydiflumetofen and Vibrance Flexi on early‐season control of blackleg using moderately resistant canola cultivar SY4135 and susceptible cultivar Westar. In the greenhouse, seedlings inoculated with green fluorescent protein (GFP)‐tagged L. maculans showed lesion development and apoplastic mycelial growth in cotyledons in control and Vibrance Flexi treatments but no lesion development or in planta mycelial growth was observed in pydiflumetofen‐treated seedlings, in Westar or SY4135, 14 days postinoculation. SY4135 and Westar plants with pydiflumetofen‐treated seeds inoculated with L. maculans isolate D3 had significantly lower disease severity. Both host genotypes treated with pydiflumetofen showed lower disease severity estimates than the other treatments. Statistically significant disease severity reduction was cultivar dependent in the field. Canola is most susceptible to blackleg as a seedling, from the cotyledon to two‐ to four‐leaf stage. Pydiflumetofen protects the plant at the critical window for infection. Therefore, pydiflumetofen could be a potential tool that farmers can add to their blackleg management toolbox. Blackleg disease severity reduction in plants raised from seeds treated with pydiflumetofen confirmed the ability of the fungicide to protect the plant at the critical window for infection under controlled and field conditions.