Anxiety disorder (AD) and Parkinson’s disease (PD) are complex neuropsychiatric and brain degenerative diseases that profoundly affect neurological function, overall health, and quality of life. Increasing clinical and experimental evidence suggests that anxiety symptoms often co-occur with Parkinson’s disease, indicating the presence of shared molecular mechanisms and interconnected neurobiological pathways. Consequently, identifying common molecular determinants and therapeutic targets is essential for improving early diagnosis, understanding disease progression, and developing effective treatment strategies. In this study, a comprehensive framework was employed to determine significant differentially expressed genes (DEGs) from publicly accessible RNA-based datasets. Functional enrichment analysis were performed to unveil the correlated genetic activities and regulatory pathways. Protein–protein interaction (PPI) structure analysis was used to locate hub genes (HGs), while gene regulatory network (GRN) were constructed to explore master regulatory mechanisms. Eventually, numerical drug repurposing study was performed to identify candidate therapeutic compounds targeting both disorders. The identified molecular signatures and candidate drugs may provide potential biomarkers and therapeutic targets for early diagnosis and improved treatment strategies for AD and PD.