Several biotic stresses threaten Triticum aestivum (wheat) plants, with fungal infections being particularly concerning. In this research, in silico data analysis was used to identify the significantly common expressed genes of wheat plants in response to fungal infections regardless of genotypes and source of pathogen as a biotic stress. Transcriptome sequencing datasets were retrieved from the Gene Expression Omnibus on the NCBI GenBank database. The selected five datasets had four different wheat genotypes as follows: two datasets featured Triticum aestivum L. genotypes infected with either Zymoseptoria tritici or Blumeria graminis; another one included the YR08 genotype infected with Puccinia striiformis; and the last dataset contained the Nobeokabouzu-komugi and Sumai3 genotypes, both infected with Fusarium graminearum. The count matrix of each dataset was employed for the downstream analysis. Furthermore, the findings demonstrated that out of the total 110,428 studied genes in the four experiments, 10,771 (9.8%) were differentially expressed, of which 6,490 (5.9%) were significantly upregulated and the remaining 4,281 (3.9%) were significantly downregulated. Eight of the significantly regulated genes showed different overlaps across the five datasets, depending on the wheat genotype and the type of fungal infection. Six of these eight genes are crucial for regulating the resistance of wheat plants to various plant pathogens. The molecular functional enrichment analysis revealed five key proteins involved in the plant defense response to fungal infections. The candidate genes identified in this study could be bioengineered to enhance the resistance of wheat varieties against fungal pathogens.