High temperature coinciding with the anthesis period in wheat is one of the major constraints in wheat production. Appropriate selection criteria help plant breeders to make maximum use of the genetic variation to improve stress tolerant in crops. Thus, the aim of the study was to explore heat stress tolerance indices in spring wheat genotypes to select the heat stress tolerant lines. In this study twenty wheat genotypes were evaluated during wheat growing season (2019–2020) under normal and late sown (heat stress) conditions. The experiment was conducted at Institute of Agriculture and Animal Science, Bhairahawa, Nepal using alpha lattice design with two replications. The results of the study reveal that the mean grain yield of all genotypes was decreased by 47.58% under stress condition as compared to normal sowing condition, suggesting significant effect of heat on grain yield. Tolerance index (TOL) and stress susceptibility index (SSI) had strong negative correlation (− 0.80 to −0.945) with grain yield (Ys) of genotypes under stress condition. Similarly, the grain yield of genotypes under both conditions was found strongly and positively correlated (0.899 to 0.965) with mean productivity (MP), geometric mean productivity (GMP) and stress tolerance index (STI). Results suggest that these indices could be used to select high yielding genotypes under both conditions. Based on principal component and biplot analysis Bhrikuti, NL1420, BL4669, NL1350 and NL1368 were found to be superior genotypes with high yielding capacity under both conditions. Thus these genotypes are potential to cultivate in heat prone areas of Nepal and can be used as genetic resources in crop improvement program.