Canola cultivation at high latitudes is becoming more promising in terms of modern climate change. Sustainable crop production requires an understanding of yield-limiting factors, which need to be adjusted in agricultural management first. Therefore, our study was aimed at examining the effect of climate and soil fertility factors on the canola yield from 2012 to 2015 in northwestern Russia. Simultaneously, effectiveness of chemical fertilizer (N65 P50 K50 and N100 P75 K75 ) rates was tested. Studied soils had light texture, high acidity and severe sulfur deficiency. Canola yield (Y) varied from 0.81 to 1.60 t·ha−1 for the observed period. Applied fertilizer increased Y by around 30%, but this change was not significant. Climate effect testing with the FAO-AquaCrop simulation showed no noticeable water and heat stresses for the study period (0% to 20% reduction in potential Y). Among the tested soil properties, the content of organic carbon, available nitrogen and sulfur significantly correlated with Y (r = 0.58–0.66). Combining these factors together with soil pH in a path model explained 60% of variability in Y. Importantly, sulfur had the highest and most significant effect in this model. Thus, this soil parameter is the main yield-limiting factor in the study area, which must be the first to be adjusted in agricultural practice.