Elevated preoperative levels of alkaline phosphatase (ALP) in patients with refractory secondary hyperparathyroidism are correlated with postoperative hypocalcemia and mortality. The aim of this study was to identify the predictors of preoperative ALP in patients with secondary hyperparathyroidism. From April 2012 to December 2015, 220 patients with refractory secondary hyperparathyroidism undergoing total parathyroidectomy without autotransplantation were reviewed. A total of 164 patients presented with elevated preoperative ALP. Univariate analysis showed that patients with elevated ALP were significantly younger. The elevated ALP group had significantly higher levels of preoperative parathyroid hormone (PTH), lower preoperative serum calcium, higher preoperative phosphorus, lower postoperative hypocalcemia, and a longer hospital stay. Logistic regression analysis showed that elevated preoperative PTH was a significant independent risk factor for elevated preoperative ALP (P = 0.000), and its value of 1624 pg/mL was the optimal cutoff point. Factors predictive of elevated preoperative ALP in patients with secondary hyperparathyroidism include preoperative PTH. Earlier surgery, aggressive calcium supplementation, and more careful or aggressive postoperative care for high-risk patients are needed.