Reported herein is an unusual case of prostatic phyllodes tumor with exuberant glandular hyperplasia that led to misdiagnosis of adenocarcinoma. The tumor was detected in a 52-year-old man who had a 1 year history of dysuria. Adenocarcinoma of the prostate was diagnosed from a needle biopsy specimen. The patient received hormonal therapy for 6 months and underwent radical prostatectomy. Histologically, the tumor had an atypical stromal cell proliferation and elongated slit-like glands characteristic of a phyllodes tumor. The tumor was also accompanied by a florid proliferation of small acini, most of which lacked basal cells, a common manifestation of adenocarcinoma in the overall tumor area. The following features of the resected tumor were helpful for concluding that these acini were benign: lack of cytological anaplasia in spite of structural atypia, presence of scattered basal cells confirmed by immunohistochemistry (high-molecular-weight cytokeratin), and histological transition from these acini to apparently benign slit-like glands. The final diagnosis was then made as 'phyllodes tumor of the prostate with exuberant glandular hyperplasia'. Atypical stromal cells might provide a clue for the recognition of this rare tumor at initial diagnosis by needle biopsy.