The aim of the present study was to compare the effects of two methods of dexmedetomidine (Dex) administration on myocardial injury, inflammation and stress in ischemic myocardium during rheumatic heart valve replacement. In total, 90 patients were included in the present study and were divided into the following three groups: i) Dex group (1.0 µg/kg Dex pre-administered 10 min prior to anesthesia, then 0.5 µg/kg/h Dex for maintenance); ii) Dex pre-conditioning group (Pre-Dex; 1.0 µg/kg Dex administered 10 min prior to anesthesia, then saline for maintenance); and iii) control group (saline 10 min prior to anesthesia and saline during maintenance), with 30 patients in each group. Heart rate (HR) and mean artery pressure (MAP) were recorded at eight time-points: i) T1, pre-medication; ii) T2, 10 min post-medication; iii) T3, immediately post-intubation; iv) T4, upon skin incision; v) T5, upon sawing the sternum; vi) T6, immediately post-cardiopulmonary bypass; vii) T7, immediately post-operation; and viii) T8, 24 h post-operation. The serum cardiac troponin I (cTnI), interleukin (IL)-8, IL-10 and malondialdehyde (MDA) levels were also detected at T1, T6, T7 and T8. Blood glucose levels were detected at T1, T5, T6 and T7. In comparison with the control group, patients in the Dex group exhibited a significant increase in cardiac function, as indicated by an increase in HR, MAP and IL-10 levels, and a significant decrease in cTnI, IL-8, MDA and glucose levels. Both Dex perfusion and Dex preconditioning were able to reduce myocardial injury, inflammation, oxidative stress and stress response in rheumatic heart valve replacement surgery. However, Dex perfusion during the whole surgery was more effective than Dex preconditioning treatment. The study was registered with the Chinese Clinical Trial Registry (ChiCTR; no. ChiCTR-INR-17011955).