Stones in the seminal vesicles are extremely rare. We present a 62-year-old patient with a stone within a seminal vesicle cyst, who was cured by laparoscopic treatment. The operative time was 80 min, and the estimated blood loss was 90 mL. Scanning electron microscope examination of the stone showed a compact crystal image externally and sparse spherical crystal structure in kernel. Composition of the stone was calcium fluorophosphate on X-ray diffractometer. The follow-up time was 15 months with no recurrence of cyst or stone. To our knowledge, this case is the first to describe laparoscopic removal of a stone within a seminal vesicle cyst, and the first to describe calcium fluorophosphate as the composition of seminal vesicle stones.