Leptosphaeria maculans causes blackleg of Brassica napus (canola), manifesting in symptoms including leaf lesions, stem canker, and root rot. Root rot is an extension of the stem canker phase of the disease resulting from foliar infection; however, the role of root rot in grain yield loss has not been investigated. Field experiments were conducted in south-eastern Australia to determine the efficacy of fungicides and host resistance to stem canker for the control of root rot, along with the association between root rot severity and grain yield. Fungicides applied as a seed dressing (fluquinconazole) or coated on fertiliser (flutriafol) reduced root rot severity by 16 and 41%, respectively. Root rot severity was 78% less in a B. napus cultivar with an Australian Blackleg Rating (ABR) of 9.0 (highly resistant to stem canker) than in a moderately resistant cultivar (ABR 5.5), and was also reduced in Brassica species with good resistance to stem canker. Root rot caused little or no additional reduction in yield or harvest index of individual B. napus plants above that caused by stem canker. Individual upright plants with greater than 80% of the stem cross-section blackened had significantly reduced seed yield; however, this was influenced by rainfall during the grain-filling period. This study shows that current management strategies for stem canker caused by L. maculans also control root rot in B. napus, as although the symptoms in roots are severe, these symptoms have no additional effect on yield.