The diagnostic work-up of cancer of unknown primary (CUP) is a challenging task; in addition, only a little data on BRAF targeting in CUP are currently available. Traditionally, the identification of favourable and unfavourable CUP subsets directs the choice of treatment. The present article reports the case of a 50-year-old male patient presenting with a BRAF-mutated CUP, a rare and generally unfavourable subset. Based on imaging, immunohistochemistry and a high value of carbohydrate antigen 19-9, an upper gastrointestinal profile was initially presumed. After disease progression on treatment with a first-line platinum-based doublet chemotherapy, a significant response was documented after treatment with the BEACON combination. The present case report highlighted the paradigm shift in diagnosis and treatment of CUP from a histology-based approach to molecular profiling with the introduction of precision medicine.