Background: Nasopharyngeal cancer (NPC) is a malignancy of the nasopharyngeal mucosal epithelium. Primary and secondary metastases in nasopharyngeal cancer are generally prevalent in the bones. Gene expression plays a critical role in regulating fundamental cellular processes in cancer cells, including metastasis. Methods: A total of 29 patients with non-metastatic NPC were included in the study. Results: The mean age of the participants was 48.45±9.98 years old. Most participants were male (75.9%). More than half of the participants had T4 and N2, 52.7% and 51.0% respectively). Secondary metastasis was observed in 9 of the 29 participants within two years. Patients with secondary metastases had a higher proportion of T4 (7/9) and N2 (4/9) disease. Bone was the first site of secondary metastasis (6/9 patients). The median time to secondary bone metastasis was 14.0 (6.8-21.2) months. Based on the differential expression gene (DEG) analysis, the MMP9 gene was upregulated 12.50 (4.18–37.40), adjusted p <0.01, and the ADNP gene was downregulated 0.141 (0.04–0.43), adjusted p 0.04, among patients with secondary bone metastasis. Conclusions: Bones are the first site of metastasis, with a time to metastasis of 14.0 (6.8-21,2) months. MMP9 was upregulated, and ANDP was downregulated in patients with bone metastasis compared to those without metastasis. © 2026, Indonesian Society of Internal Medicine. All rights reserved.