The sunflower, an important oilseed crop and food source across the world, is susceptible to several pathogens, which cause severe losses in sunflower production. The utilization of genetic resistance is the most economical, effective measure to prevent infectious diseases. Based on the sunflower pangenome, in this study, we explored the variability of resistance gene analogs (RGAs) within the species. According to a comparative analysis of RGA candidates in the sunflower pangenome using the RGAugury pipeline, a total of 1344 RGAs were identified, comprising 1107 conserved, 199 varied, and 38 rare RGAs. We also identified RGAs associated with resistance against Sclerotinia sclerotiorum (S. sclerotiorum) in sunflower at the quantitative trait locus (QTL). A total of 61 RGAs were found to be located at four quantitative trait loci (QTLs). Through a detailed expression analysis of RGAs in one susceptible and two tolerant sunflower inbred lines (ILs) across various time points post inoculation, we discovered that 348 RGAs exhibited differential expression in response to Sclerotinia head rot (SHR), with 17 of these differentially expressed RGAs being situated within the QTL regions. In addition, 15 RGA candidates had gene introgression. Our data provide a better understanding of RGAs, which facilitate genomics-based improvements in disease resistance in sunflower.