Background Cardiovascular diseases have the highest mortality rates and the costs for treatment are very high so far. Cardiovascular rehabilitation helps to reduce the risk of relapses or deterioration of cardiovascular diseases, however, the number of patients that participate is insufficient, especially in later stages of the rehabilitation process. The aim of the study is to evaluate cost-effectiveness of cardiovascular rehabilitation care using cost-utility analysis. Methods The study evaluate the Cardio ambulance Late Phase, Late Phase of The Spa treatment and for comparison also Early Phase of The Spa treatment in Konstantin Spa. The research was conducted in outpatient facility and spa facility. For QALY, a prospective questionnaire survey was conducted in patients with cardiovascular disease using generic EQ-5D-5L questionnaires. The costs were calculated from the perspective of the health care payer. The cost-utility analysis was carried out at the end of the study and results are presented in incremental cost-utility ratio. Results The average cost per patient in outpatient facility is CZK 12,459. The average amount for an overall early phase of spa treatment per patient is CZK 35,161. The average amount for an overall late phase spa treatment per patient is CZK 30,503. QALY obtained from Index Value was 0.092 (Konstantin Spa Early Phase), 0.054 (Konstantin Spa Late Phase), 0.26 (Cardio ambulance Late Phase). For Konstantin Spa Late Phase, the ICUR value was 644,436 and for Konstantin Spa Early Phase was 343,981 (comparator is the Cardio ambulance Late Phase). Konstantin Spa Early Phase compared to Konstantin Spa Late Phase had an ICUR value of 122,592. Conclusions The results of this study suggest that the spa treatment in later stage of the cardiovascular rehabilitation process is cost effective with use of cost effectiveness threshold three times the Gross Domestic Product (GDP) per capita.