Genetic architecture of seedling drought tolerance is complex and needs to be better understood. To address this challenge, we developed a protocol to identify the most promising drought-tolerant genotypes at the seedling stage in winter wheat. A population of 146 recombinant inbred lines (F9) derived from a cross between wheat cultivars, ‘Harry’ (seedling drought tolerant) and ‘Wesley’ (seedling drought susceptible) were used in this study. All genotypes were sown in three replications in a randomized complete block design under controlled conditions in a greenhouse. Seven traits were scored and grouped into tolerance traits; days to wilting, leaf wilting, and stay green and survival traits; days to regrowth, regrowth, drought survival rate, and recovery after irrigation. Three selection indices were calculated (1) tolerance index, (2) survival index, and (3) drought tolerance index (DTI). The same set of genotypes were also tested for grain yield in two low rainfall environments for two seasons. High genetic variation was found among all genotypes for all seedling traits scored in this study. Correlations between tolerance and survival traits were weak or did not exist. Heritability estimates ranged from 0.53 to 0.88. DTI had significant phenotypic and genotypic correlations with all seedling traits. Genotypes were identified with a high drought tolerance at the seedling stage combined with high grain yield in low rainfall. Breeding for tolerance and survival traits should be taken into account for improving winter wheat drought tolerance at seedling stage. The selected genotypes can be used for to further improve drought tolerance in high yielding wheat for Nebraska.