The Milu deer ( Elaphurus davidianus ), also known as Père David's deer, has experienced severe population bottlenecks. While infectious diseases are closely monitored, baseline data on sporadic non-communicable diseases, such as neoplasia, remain scarce for wildlife disease surveillance. To date, the molecular mechanisms driving spontaneous tumorigenesis in this species remain uncharacterized. This study provides the first integrated characterization of a single facial tumor in the Milu deer, combining histopathological analysis, whole-genome sequencing (WGS), and RNA sequencing (RNA-seq). Histopathological analysis confirmed that the tumor is an epithelial neoplasm exhibiting significant mesenchymal features, indicative of epithelial-mesenchymal transition (EMT). RNA-seq differential expression analysis identified 6,537 differentially expressed genes (DEGs), while WGS revealed 114 high-confidence, tumor-specific non-synonymous somatic mutations. Functional enrichment analysis demonstrated that oncogenesis in this specific specimen is potentially driven by dysregulated cell cycle, cytoskeletal reorganization, and metabolic reprogramming mediated by PI3K-Akt and mTOR signaling. Notably, the human papillomavirus (HPV) infection pathway emerged as significantly enriched among the DEGs. We emphasize that this enrichment does not provide evidence of viral involvement, as no direct viral detection was performed; rather, it exclusively reflects the severe dysregulation of highly conserved host cellular networks implicatedin cell cycle, apoptosis, and immune regulation. By integrating mutational and transcriptomic data, we prioritized ten putative tumor-associated genes, including LGALS3, DMBT1, CHAF1A, GON4L , and SIRPA , which are linked to metastasis, immunosuppression, and proliferation. This case study provides the first integrated molecular profile of a facial tumor in the Milu deer, offering critical insights for health management of this endangered species and establishing a novel framework for comparative oncology that will inform future clinical diagnoses of neoplasms in this population.