Introduction Atrial fibrillation (AF) is the most common arrhythmia affecting patients in open heart ICU after coronary artery bypass grafting (CABG). Most cardiac surgery textbooks recommend beta blockers as the drug of choice for treating such a condition while many experienced physicians and a number of anesthesiology references offer amiodarone as the drug of choice. Therefore, because of insufficient evidence and the aforementioned controversy, we decided to conduct a study evaluating these two antiarrhythmic medicines. Methods This is a double-blind, randomized, clinical trial performed on patients admitted for CABG at Amir al Momenin hospital in Arak province, Iran, who developed new onset AF after surgery. Based on the type of medication used, these patients were randomly divided into two groups: amiodarone (A) group and metoprolol (M) group. Each group consisted of 73 cases. All data were analyzed via SPSS 19. Results Among the results achieved in this study, amiodarone was successful in treating AF in 55 patients (73%), while metoprolol achieved normal rhythm in treating AF in 69 patients (92%). With a p-value of 0.04, it seems that metoprolol is more effective in treating AF. Conclusion Metoprolol seems to be a most efficacious medication for post-CABG AF (p-value = 0.004).