HPV16 is the primary etiological factor for cervical cancer, with typical mutations that have varied geographical distributions and carcinogenic potency. Detecting HPV16 mutations, therefore, has consequences for cervical cancer screening, clinical diagnosis, and therapy. In Vietnamese women with cervical cancer, HPV16-positive samples were analyzed for nucleotide sequence alterations using Sanger sequencing of the E6, E7, and L1 genes. The HPV16 variants were identified using ATGC 7.2, and the phylogenetic tree was constructed using MEGA 11.0.10. Among 180 patients infected with HPV, 76.1% revealed single infections, and 24.9% showed multiple infections. The most common HPV genotypes were HPV16 (63.9%), HPV18 (26.7%), and other HPV (6.9%). HPV16 alterations were found in all E6, E7, and L1 genes, with 15 missense and 18 synonymous mutations. Missense mutations include: R10G, Q14H, D25E, H78Y, L83V (E6); M29V, R35K, L78R, L95P (E7); H73Y, T176N, N178T, T317P, T386S, L472F/I (L1). HPV16 sublineages include A1 (17.2%), A2 (0.9%), A3 (56.0%), A4 (19.0%), D1 (4.3%), and D3 (2.6%). Our findings showed that HPV16 is prevalent in cervical cancer in Vietnam, with the European lineage distribution predominating. Although HPV16 is responsible for a significant number of cervical cancers, the L83V mutation rate is only observed in 6.9% of samples.