Sclerotinia sclerotiorum, a necrotrophic fungal pathogen, infects more than 400 plant species globally, resulting in significant yield loss in the US annually. Challenges in controlling these diseases arise from the quantitative resistance displayed by host plants, with most commercial crop varieties lacking adequate resistance. Previous GWAS identified several WRKY transcription factors associated with S. sclerotiorum resistance. Preliminary evaluations of T-DNA insertional mutants indicated that wrky3 and wrky4 mutants are hypersusceptible to S. sclerotiorum while wrky27 mutants exhibited increased resistance. This study aimed to elucidate WRKY3, 4, and 27 roles in S. sclerotiorum resistance. Overexpressing WRKY4 in Arabidopsis showed increased resistance against S. sclerotiorum. The differential expression analysis revealed WRKY27 downregulation during infection. Additionally, sunflower orthologs displayed differential expression notably HaWRKY3-1,3-2,3-3 and HaWRKY27 upregulation in resistant lines. These findings contribute to understanding the molecular mechanisms underlying host resistance to S. sclerotiorum, offering insights for enhancing host resistance against this pathogen.