Wheat stripe rust is a devastating fungal disease that threatens most of the world’s wheat production. New resistance genes must be identified and introgressed into future wheat cultivars to tackle the current and newly emerging races of this pathogen. In this study, we conducted a genome-wide association study (GWAS) using 9523 single nucleotide polymorphism (SNPs) markers identified from 245 wheat lines to understand the genetic basis of stripe rust resistance. The field trial that was carried out for two consecutive years (2018/2019) at Kulumsa Agricultural Research Center revealed that the majority of the lines were resistant/moderate resistance with high heritability estimates. The GWAS analysis identified 96 marker-trait associations (MTAs) distributed across 23 loci based on –log10 (p) ≥ 2.5 threshold value. These markers were characterized as two major, eight nominal, and thirteen suggestive QTLs. Of these, 63 SNPs were located on 7B and 6B chromosomes, while the remaining 33 SNPs were distributed across ten chromosomes (1B, 2A, 2B, 3B, 4A, 4B, 5A, and 5B). Among the 23 QTLs, eight (EWYY1B.4, EWYY2A, EWYY4A, EWYY5A.1, EWYY5A.2, EWYY5B.2, EWYY6B.1, and EWYY7B.3) were mapped far from previously known resistance genes and maybe novel loci associated with wheat stripe rust resistance. These loci could be useful for wheat stripe rust resistance development through marker-assisted selection and will broaden the genetic bases of currently cultivating wheat cultivars. The thirty-six lines which were conferred immune/resistance based on field study across both seasons are recommended to be used in the national wheat breeding programs.