Paragangliomas of the urinary bladder are rare neoplasms derived from chromaffin tissue with a chromosomal imbalance. Their preoperative diagnosis and assessment of malignant potential remain significant challenges for urologists. The current report presents the case of a 34-year-old male who presented with a history of paroxysmal gross hematuria lasting for 7 months. Chromosome duplications were detected by fluorescence in situ hybridization (FISH) in urine exfoliated cells, and the diagnosis was confirmed by histopathology following a transurethral resection. To the best of our knowledge, this is the first reported case of urinary bladder paraganglioma in which chromosomal duplications were detected by FISH in urine exfoliated cells. This may be helpful to its differential diagnosis and malignant potential determination.