OBJECTIVES: To understand from the perspective of the Brazilian National Health System (SUS) the cost-effectiveness of treating secondary hyperparathyroidism with IV paricalcitol versus IV calcitriol in dialysis patients diagnosed with end stage chronic kidney disease. METHODS: A decision-analytic Markov model comparing the use of IV paricalcitol versus calcitriol. Main outcomes include parathyroidectomy, hospitalizations or death, life time costs and the results are reported as incremental cost-effectiveness ratios (ICER). The treatment costs are based on the DATASUS administrative claim database  which includes individuals with an end stage chronic kidney disease secondary hyperparathyroidism diagnosis, who underwent hemodialysis at SUS, from 2009 to 2012. The main clinical outcomes are based on clinical trials or cohort studies reporting those outcomes. RESULTS: The reference case analysis was a 5-year time horizon based on a comparison of treatment with paricalcitol versus calcitriol, of end stage chronic kidney disease secondary hyperparathyroidism dialysis patient. The use of paricalcitol leads to savings amounting R$ 113.999.601,06  to SUS and an increase in life-years gained (0.52 years). Paricalcitol was dominant over the comparator (calcitriol), indicating better health outcomes and lower costs. One-way sensitivity analyses and probabilistic sensitivity analyses confirmed the robustness of the model. CONCLUSIONS: In our model the substitution of IV calcitriol by IV paricalcitol can be a more cost-effective choice in the management of secondary hyperparathyroidism.