Wheat is one of main cultivated crop in worldwide for human nutrition. However, its yield is frequently threatened by nitrogen stress. Hence to ensure food security for the rapidly increasing population, improving nitrogen use efficiency (NUE) to increase wheat yield has great practical significance. A comparative transcriptomic study was carried out through RNA-seq analysis to investigate the gene expression that regulate NUE, in N-efficient (PBW677) and N-inefficient (PBW703) cultivar under nitrogen (N) stress. Differentially expressed genes (DEGs) were classified based on their statistical significance (p ≤ 0.05) and up-regulation with ≥ 2 log2 fold change (FC) and down-regulation with ≤ −2 log2 FC values. RNA-seq data revealed a total of 2,406 differentially expressed genes (DEGs) present in the both contrasting cultivars under N stress. The efficient genotype PBW677 had considerably more abundant DEGs as 1653 (903 root+750 shoot) than inefficient cultivar PBW703 as 753 (96 root+657 shoot. Gene ontology enrichment and pathway analysis of these DEGs suggested that the two cultivars differed in terms of adaptive mechanism. Predominant upregulation and downregulation of certain genes involved in metabolic pathways was the key adaptive feature of both cultivars indicating their energy consuming approach in adaptation under nitrogen stress. Potentially expressed DEGs in response to N stress were identified that are involved in N assimilation and carbon metabolism along with transcription factors; transporter and protein kinases were highlighted. The identified TF belonged to different families, including MYB, WRKY, RING finger protein, Zinc finger protein, TIFY proteins , AP2/ERF, HSP/HSF, , NDR1/HIN1domain, bZIP ,GATA, bHLH and ARF, reported to be associated with stress defense, were showed higher differentially expression in efficient cultivar. Besides, transporters genes related to Zinc, ABC, amino acid, sugar, and calcium in response to N-stress have showed differential expression in efficient cultivar than inefficient one These results suggested that PBW677 cultivar expressed potential candidate genes that improves its nitrogen use efficiency.