Drought and heat stress are major challenges to crop productivity, especially in semi-arid regions with limited water and erratic rainfall. Pearl millet, the sixth most widely cultivated cereal for food, forage, and feed, has emerged as a promising climate-resilient crop to address these challenges. However, the genomic regions associated with its drought-tolerance remain largely unknown. This study utilizes genome-wide association analysis (GWAS) to identify drought related quantitative trait nucleotides (QTNs) in 187 pearl millet germplasms, genotyped using genotyping-by-sequencing (GBS), yielding 35,071 high-quality single nucleotide polymorphic (SNP) markers. Phenotypic variation was observed between irrigated and rainfed treatments, and the stress tolerance index (STI) derived from these data was used for GWAS. Ninety-five QTNs were mapped across all seven chromosomes using four GWAS models (MLMM, FarmCPU, Blink, and 3VmrMLM). These QTNs colocalized in close proximity with 86 candidate genes, including PMF1G04719 and PMF2G07960 (rubisco binding protein), PMF1G07862 (actin-7). These were involved in drought response mechanisms, such as reactive oxygen species (ROS) scavenging, and abscisic acid signaling pathway. Candidate gene haplotype analysis, complemented by in silico expression profiling under drought stress using milletdb, identified 11 highly expressed candidate genes. These candidate genes represent promising targets for further functional validation and breeding efforts. Overall, these findings provide valuable genetic and genomic resources for improving pearl millet for climate resilience and sustainable production in semi-arid regions.