Pleomorphic adenoma (PA) is the most common benign salivary gland tumor. Fine‐needle aspiration (FNA) of PA exhibits variable combinations of bland ductal epithelial cells, myoepithelial cells, and characteristic magenta fibrillary stroma on Diff–Quik/Romanowsky stain. However, a cellular PA with scant chondromyxoid stroma can be a diagnostic challenge on FNA. Around 70% of PAs have a translocation involving PLAG1 or HMGA2. The presence of either PLAG1 or HMGA2 fusion gene can be used to diagnose PA since they have not been reported in other salivary gland tumors except for carcinoma ex PA. In this case report, we describe a case of cellular PA initially diagnosed on FNA as a “low grade salivary gland neoplasm, favor PA.” RNA next‐generation sequencing performed on the cell block showed a BOC‐PLAG1 fusion gene. The presence of PLAG1 fusion gene in conjunction with cytomorphology supported a diagnosis of PA. The mass was surgically removed and proved to be a cellular PA with scattered foci of chondromyxoid and collagenous stroma. To our knowledge, this is the first reported PA bearing BOC‐PLAG1. RNA next‐generation sequencing performed on cytology specimens can be helpful in achieving a more specific diagnosis of salivary gland tumors.