Continuous development of high yielding FHB-resistant wheat varieties is a top priority for wheat breeding programs. Since selection for FHB-resistance under field conditions remains a challenge due to the scale of manual phenotyping required and potential subjectivity in selection criteria, an on-ground plot-level infrared thermal imaging was carried out during the on-set of FHB-infection in 2022 and 2023. Plot Level infrared thermal readings showed significant correlation with FHB-Severity, FHB-Incidence and FHB-Index. K-Means clustering grouped a larger portion of the evaluated genotypes with susceptible genotype Ambassador in both years. Since Infrared Thermal Imaging was able to delineate FHB-resistance among breeding lines, we conducted genome wide association for FHB-related traits and infrared thermal readings. Significant SNPs associated with FHB Severity were mapped in chromosomes 2A, 3A, 3B, 4A, 5A, 7A, 7B, and 7D, while significant SNPs in chromosomes 2A, 5A, 6A, and 7A were mapped for FHB Index. We found a significant SNP coming from chromosome 2B associated with field level infrared thermal reading co-localized with a previously reported QTL for FHB resistance. Based on the results, infrared thermal imaging showed higher capacity to identify susceptible genotypes over FHB-Index. Further, incorporating infrared thermal imaging increases efficiency and intensity in selecting putative FHB-resistant wheat genotypes. Lastly, the study showed the potential integration of infrared thermal imaging with genome wide association studies in identifying putative SNPs associated with FHB Resistance.