Sclerotinia stem rot (SSR) caused by the necrotrophic fungus is a major disease in rapeseed () worldwide. Breeding for SSR resistance in , as in other crops, relies only on germplasms with quantitative resistance genes. A better understanding of the genetic basis for SSR resistance in thus holds promise for the genetic improvement of disease resistance. In the present study, a genome-wide association study (GWAS) for SSR resistance in were performed using an association panel of 448 accessions genotyped with the 60K Infinium single-nucleotide polymorphism (SNP) array. A total of 26 SNPs corresponding to three loci, , , and were associated with SSR resistance. Haplotype analysis showed that the three favorable alleles for SSR resistance exhibited cumulative effects. After aligning SSR resistance quantitative trait loci (QTL) identified in the present and previous studies to the reference genome, one locus () was found to be located within the confidence interval of a QTL identified in previous QTL mapping studies and another two loci ( and ) were considered novel loci for SSR resistance. A total of 39 candidate genes were predicted for the three loci based on the GWAS combining with the differentially expressed genes identified in previous transcriptomics analyses.