Objective: Alzheimer’s disease (AD) is a severe neurodegenerative disorder and has become a global public health problem. Intensive research has been conducted for AD. But the pathophysiology of AD is still not elucidated. Disease comorbidity often associates diseases with overlapping patterns of genetic markers. This may inform a common etiology and suggest essential protein targets. US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) collects large-scale post-marketing surveillance data that provide a unique opportunity to investigate disease co-occurrence pattern. We aim to construct a heterogeneous network that integrates disease comorbidity network from FAERS with protein-protein interaction to prioritize the AD risk genes using network-based ranking algorithm. Materials and Methods: We built a disease comorbidity network (DCN) based on indication data from FAERS using association rule mining. DCN was further integrated with protein-protein interaction network. We used random walk with restart ranking algorithm to prioritize AD risk genes. Results: We evaluated the performance of our approach using AD risk genes curated from genetic association studies. Our approach achieved an area under a receiver operating characteristic curve (AUROC) of 0.770. Top 500 ranked genes achieved 5.53-fold enrichment for known AD risk genes as compared to random expectation. Pathway enrichment analysis using top ranked genes revealed that two novel pathways, ERBB and coagulation pathways, might be involved in AD pathogenesis. Conclusion: We innovatively leveraged FAERS, a comprehensive data resource for FDA post-market drug safety surveillance, for large-scale AD comorbidity mining. This exploratory study demonstrated the potential of disease-comorbidities mining from FAERS in AD genetics discovery.