Introduction: Treatment of urinary tract calculi in patients with Ehlers-Danlos syndrome, a connective tissue disorder, has rarely been reported. Case presentation: A 33-year-old woman with Ehlers-Danlos syndrome sought evaluation of right-sided abdominal pain from her family physician. Right-sided hydronephrosis was noted and she was referred to our hospital for further evaluation and treatment. A ureteral calculus with a maximum diameter of 8 mm was demonstrated at the right ureterovesical junction. Transurethral lithotripsy was performed under general anesthesia without complications. Conclusion: Lithotripsy may be safely performed in patients with Ehlers-Danlos syndrome.