Terminal drought stress poses a big challenge to sustain wheat grain production in rain-fed environments. This study aimed to utilize the genetically diverse pre-breeding lines for identification of genomic regions associated with agro-physiological traits at terminal stage drought stress in wheat. A total of 339 pre-breeding lines panel derived from three-way crosses of ‘exotics × elite × elite’ lines were evaluated in field conditions at Obregon, Mexico for two years under well irrigated as well as drought stress environments. Drought stress was imposed at flowering by skipping the irrigations at pre and post anthesis stage. Results revealed that drought significantly reduced grain yield (Y), spike length (SL), number of grains spikes−1 (NGS) and thousand kernel weight (TKW), while kernel abortion (KA) was increased. Population structure analysis in this panel uncovered three sub-populations. Genome wide linkage disequilibrium (LD) decay was observed at 2.5 centimorgan (cM). The haplotypes-based genome wide association study (GWAS) identified significant associations of Y, SL, and TKW on three chromosomes; 4A (HB10.7), 2D (HB6.10) and 3B (HB8.12), respectively. Likewise, associations on chromosomes 6B (HB17.1) and 3A (HB7.11) were found for NGS while on chromosome 3A (HB7.12) for KA. The genomic analysis information generated in the study can be efficiently utilized to improve Y and/or related parameters under terminal stage drought stress through marker-assisted breeding.