Osteoporotic fracture associated with calcium dysregulation is more common in patients with kidney stones. However, little is known about the association of kidney stones and bone health status in patients with chronic kidney disease (CKD). This retrospective medical record-based study included 2282 patients with stable stage 3-4 CKD between 2007 and 2017. Of these, 113 patients were diagnosed with kidney stones. Propensity score matching for 226 patients with and without kidney stones showed that osteoporotic fracture occurred more often in patients with kidney stones (33, 29.2%) than in patients without kidney stones (16, 14.2%), resulting in rates of 5.56 and 2.63/100 patient-years, respectively (p < 0.01). In particular, Cox proportional hazard analysis revealed that kidney stones were significantly associated with osteoporotic fracture, even after adjusting for age, sex, body mass index, kidney stones, estimated glomerular filtration rate, excessive alcohol consumption, current smoking, and steroid use in patients with CKD stage 3-4 (hazard ratio, 2.32, 95% CI 1.24-4.34, p = 0.01). This study showed that the presence of kidney stones was a significant predictor for osteoporotic fracture in patients with CKD, suggesting that it should be considered as a clinical risk factor for osteoporotic fracture in them.