High recurrence rates and poor survival rates for late stage/advanced temporal bone squamous cell carcinoma with the standard treatments continues to be a significant challenge to otolaryngologists. Targeted therapy for temporal bone squamous cell carcinoma after relapse has not been reported. Here we present a 58-year-old man who was diagnosed with recurrent temporal bone squamous cell carcinoma and treated with a regimen developed using whole exome sequencing. Somatic mutations in genes encoding catenin beta 1 and vascular endothelial growth factor receptor 2 were identified in the patient’s tumor sample compared to the normal tissue. The patient was then treated with Bevacizumab in combination with pemetrexed. After two weeks of treatment, tumor volume was reduced by 95% measured by MRI, and the Visual Analogue Scale headache scores went down from 10/10 to 2/10. Our results reveal novel gene mutations of temporal bone squamous cell carcinoma and demonstrate, for the first time, an effective targeted therapy for temporal bone squamous cell carcinoma. The successful treatment regimen of bevacizumab and pemetrexed may provide a new treatment option for treating recurrent temporal bone squamous cell carcinoma that fails to respond to conventional tumor resection, radiotherapy, and/or chemotherapy.