Background The optimal timing of treatment with vitamin D therapy for patients with chronic kidney disease (CKD), vitamin D insufficiency, and secondary hyperparathyroidism (SHPT) is a pressing question in nephrology with economic and patient outcome implications. Objective The objective of this study was to estimate the cost-effectiveness of earlier vitamin D treatment in CKD patients not on dialysis with vitamin D insufficiency and SHPT. Design A cost-effectiveness analysis based on a Markov model of CKD progression was developed from the Medicare perspective. The model follows a hypothetical cohort of 1000 Stage 3 or 4 CKD patients over a 5-year time horizon. The intervention was vitamin D therapy initiated in CKD stages 3 or 4 through CKD stage 5/end-stage renal disease (ESRD) versus initiation in CKD stage 5/ESRD only. The outcomes of interest were cardiovascular (CV) events averted, fractures averted, time in CKD stage 5/ESRD, mortality, quality-adjusted life years (QALYs), and costs associated with clinical events and CKD stage. Results Vitamin D treatment in CKD stages 3 and 4 was a dominant strategy when compared to waiting to treat until CKD stage 5/ESRD. Total cost savings associated with treatment during CKD stages 3 and 4, compared to waiting until CKD stage 5/ESRD, was estimated to be $19.9 million. The model estimated that early treatment results in 159 averted CV events, 5 averted fractures, 269 fewer patient-years in CKD stage 5, 41 fewer deaths, and 191 additional QALYs. Conclusions Initiating vitamin D therapy in CKD stages 3 or 4 appears to be cost-effective, largely driven by the annual costs of care by CKD stage, CV event costs, and risks of hypercalcemia. Further research demonstrating causal relationships between vitamin D therapy and patient outcomes is needed to inform decision making regarding vitamin D therapy timing.