Hypercalcemia is occasionally found in newborns with subcutaneous fat necrosis and carries potential life-threatening risk. Bisphosphonates have been recently introduced in the treatment of subcutaneous fat necrosis in newborns. We report a case of extensive subcutaneous fat necrosis in a female infant complicated with intractable hypercalcemia. Standard treatment for hypercalcemia was given, including saline hydration, a low calcium diet, furosemide, and glucocorticoid, but without response. Serum 1,25-dihydroxyvitamin D level was elevated at 126 pg/mL, 25-hydroxyvitamin D level was normal, and intact parathyroid hormone was suppressed at < 1 pg/mL. Oral clodronate disodium, a second-generation bisphosphonate, was administered, and resulted in the normalization of serum calcium, urine N-telopeptide, urine calcium/creatinine ratio, and serum intact parathyroid hormone level. This case suggests that oral clodronate may be an effective treatment for subcutaneous fat necrosis with hypercalcemia in newborns.