Winter oilseed rape (Brassica napus L.) is the main source of domestic oil in central and northern Europe, bringing profits to farmers, but the plants are often damaged by stem canker, caused by two fungal species belonging to the genus Leptosphaeria. Due to environmental concerns, the benefits of fungicide applications must outweigh disadvantages. The aim of this work was to determine the effect of stem canker on seed yield and its quality and find out the best timing of fungicide application. The multi-year field experiments were done at two sites in south-west Poland, where the disease is regarded as a serious problem. The fungicide treatments with the azole-containing preparation followed the same scheme each year; a single application was made at one-week intervals, starting in late September through mid-November for a total of eight treatments. Seed yield, oil and protein content, mass of thousand seeds as well as indole-and alkenyl-glucosinolate contents in seeds were statistically unrelated with the incidence and severity of phoma leaf spotting and stem canker symptoms. The significant decrease of the seed yield was observed in three (site × year combinations) of eight, in which phoma leaf spotting and stem canker were severe. Yield loss was noted only in years with warm and wet autumns, when cumulative mean temperatures between BBCH14 and BBCH19 plant growth stages exceeded 60 °C and precipitation in this period exceeded 110 mm of rain. Under these conditions, fungicide treatments were highly effective when they were done between BBCH15–BBC16 growth stages (5–6 true leaves).