Understanding molecular basis of drought tolerance is important for improving wheat adaption to water-deficit environments. Stem elongation stage is a key period for wheat development and determination of potential grain number. In this study, RNA-seq analysis was conducted to study the effect of drought on wheat transcriptome changes during early stem elongation stage under field condition. In total, 5776 genes responded to drought at stem elongation stage. Seven pathways were significantly affected by drought, including “phagosome”, “Spliceosome”, “Peroxisome”, “Pentose phosphate pathway”, “Ribosome”, “Cutin, suberine and wax biosynthesis”, and “RNA transport”. Real-time quantitative PCR (RT-qPCR) analysis confirmed the involvement of genes encoding tubulins, 6-phosphogluconate dehydrogenase (PGD6), cuticular wax-associated proteins, and heat shock proteins in drought tolerance under multiple genetic backgrounds. Ongoing functional analyses of candidate genes will assist unraveling their biological roles in drought tolerance in wheat.