The Cancer Genome Atlas (TCGA) sequencing analysis of head and neck squamous cell carcinoma (HNSCC) recently reported on gene fusions, however, few human papillomavirus (HPV) positive samples were included, and the functional relevance of identified fusions was not explored. We therefore performed an independent analysis of gene fusions in HPV‐positive oropharyngeal SCC (OPSCC). RNA sequencing was performed on 47 HPV‐positive OPSCC primary tumors and 25 normal mucosal samples from cancer unaffected controls on an Illumina TruSeq platform. MapSplice2 was used for alignment and identification of fusion candidates. Putative fusions with less than five spanning reads, detected in normal tissues, or that mapped to the same gene were filtered out. Selected fusions were validated by RT‐PCR and Sanger sequencing. Within 47 HPV‐positive OPSCC tumors, 282 gene fusions were identified. Most fusions (85.1%) occurred in a single tumor, and the remaining fusions recurred in 2–16 tumors. Gene fusions were associated with significant up regulation of 16 genes (including EGFR and ERBB4) and down regulation of four genes (PTPRT, ZNF750, DLG2, SLCO5A1). Expression of these genes followed similar patterns of up regulation and down regulation in tumors without these fusions compared to normal tissue. Five of six gene fusions selected for validation were confirmed through RT‐PCR and sequencing. This integrative analysis provides a method of prioritizing functionally relevant gene fusions that may be expanded to other tumor types. These results demonstrate that gene fusions may be one mechanism by which functionally relevant genes are altered in HPV‐positive OPSCC. What's new? The Cancer Genome Atlas (TCGA), a national sequencing project to investigate genetic changes in cancer, predicted the presence of nearly 14,000 gene fusion events in head and neck squamous cell carcinoma (HNSCC). Now, a major challenge is to determine which of those fusions are functionally relevant. Here, in an independent cohort of human papillomavirus (HPV)‐positive oropharyngeal SCCs, some 282 gene fusions, 10 of which overlapped with previous TCGA findings, were identified by RNA sequencing. While fusions were limited to a small number of tumors, fusion‐associated changes in gene expression were pervasive. Moreover, gene expression analyses illuminated potential functional roles for identified fusions.