Background—Patients with Chagas cardiomyopathy (CC) have high mortality, and CC is a common indication for heart transplantation (HTx) in endemic countries. Chagas disease reactivation (CDR) is common after transplantation and is likely to cause adverse outcomes unless detected and treated appropriately. This study reviews our experiences with HTx among patients with CC, and the use of benznidazole (BZ) before transplantation. Methods—During the 18-year period from 1996 through 2014, 70 of 353 patients who underwent HTx (19.8%) had CC, and 53 patients met the inclusion criteria. The effectiveness of prophylactic treatment with BZ (dose of 5 mg/kg/day, two times per day, for at least four weeks and for a maximum of eight weeks) was determined based on the observed reduction in the incidence of CDR during the post-HTx period. Results—Prophylactic therapy was administered to 18/53 patients (34.0%). During the follow-up period, the incidence rate of CDR in our study was 34.0% (18/53). Based on logistic regression analysis, only prophylaxis (OR = 0.12; CI 0.02–0.76; p = 0.025) was considered to protect against CDR. Conclusion—Our study suggests that the use of BZ may reduce the incidence of CDR in patients undergoing HTx and warrants further investigation in a prospective, randomized trial.