Lymph node (LN) metastasis is an important factor in determining the treatment and prognosis of oropharyngeal squamous cell carcinoma (OPSCC). Here, we compared the somatic mutational profiles and clonal evolution of primary and metastatic LNs using multiregion sequencing of human papilloma virus (HPV)‐positive OPSCC and HPV‐negative OPSCC. We performed high‐depth whole‐exome sequencing (200×) of 76 samples from 18 patients with OPSCC (10 HPV‐positive and 8 HPV‐negative), including 18 primary tumor samples, 40 metastatic LN samples, and 18 normal tissue samples. Among 40 metastatic LNs, 22 showed extranodal extension (ENE). Mutation profiles of HPV‐positive OPSCC and HPV‐negative OPSCC were similar to those reported previously. Somatic mutations inCDKN2AandTP53were frequently detected in HPV‐negative OPSCC. Somatic mutations in HPV‐positive OPSCC samples showed APOBEC‐related signatures. Somatic mutations from metastatic LNs showed a different pattern than the primary tumor. Somatic mutations acquired in the WNT pathway during metastasis showed a significant relationship with ENE. Clonal evolution analysis of primary and metastatic LNs showed that, in some cases, each metastatic LN originated from a different primary tumor sub‐clone.