Pulmonary arterial hypertension (PAH) is biggest preventable cause of early deaths, and hence one of the global preferences of World Health Organization for determent. PAH also induces the vast majority of patients with chronic kidney disease (CKD). Both PAH and CKD are inherently connected, but the common molecular pathways and genes of these two disorders have not yet been demonstrated. In this study, we aimed to determine the similar molecular pathways and therapeutic hub proteins in PAH and CKD that may be used to anticipate the progression of the disease. We used Limma package to conduct differential analysis of gene transcripts of PAH and CKD obtained from the Gene Expression repository. The functional annotations of the genes were determined with the use of pathway analysis. Then proteinâprotein interaction (PPI) networks were constructed to determine the hub proteins, and a clustering technique was applied to determine the most significant PPI elements. We separately evaluated the PAH and CKD gene expression-based datasets and discovered 30 differentially expressed genes (DEGs) shared by both PAH and CKD. The pathways of KEGG revealed that the most prevalent DEGs are associated with the Malaria and African trypanosomiasis. Gene ontology (GO), TF and miRNA analysis and module investigation is treated the forthcoming work of this study. Finally, various drug compounds have been suggested based on the concordant DEGs.