Aim: This study evaluates and correlates the number of myocarditis focuses and production of cytokines in Rattus norvegicus (Wistar lineage), experimentally infected with T. Cruzi and treated with Phosphorus. Methods: In two blind, controlled and randomized trials, 53 45-day-old, male animals were allocated into groups Control (n = 24): Control group infected and treated with 7% hydroalcoholic solution, the preparation vehicle of the test medication; and Phosphorus (n = 24 on days 0, 5, 10 and 24 after infection): group infected and treated with Phosphorus 13cH, diluted 10−26 and dynamized (test medication). The animals were inoculated intraperitoneally with 5 × 106 blood trypomastigotes of T. cruzi-Y strain. The medication was administered overnight (16 consecutive hours), diluted in water (1 mL/100 mL) in amber water bottles. The animals were treated 2 days before and 2, 4, and 6 days after infection. Enumeration of inflammatory foci in cardiac tissue (Hematoxylin-Eosin) and dosage of cytokines TNF-α and IFN-γ in the serum were performed on days 0, 5, 10 and 24 after infection, using three animals/group. Mann-Whitney, Friedman ANOVA, Spearman correlation (p < 0.05), and Statistica Single User Software version 13.2 were used for data analysis. Results: The animals treated with Phosphorus 13cH had high concentration of INF-ɣ on the 5th day of infection with significant decrease on the 10th and 24th days (p < 0.05), and high concentration of TNF-α on the 5th and 10th days of infection with decrease on the 24th day (p < 0.05). The treatment with Phosphorus caused a significant increase of INF-ɣ and TNF-α on the 5th day of infection compared with the Control (p < 0.05), with reestablishment on the 24th day, as well as in the Control group. The group treated with Phosphorus had 52.5% less number of myocarditis focuses in heart than Control group (p < 0.05) on the 10th day of infection. The significant increase in cytokines on the5th day of infection in the Phosphorus group is related to a significant decrease in the number of inflammatory foci in cardiac tissue on the 10th day of infection in this group. Discussion and conclusion: Treatment with Phosphorus 13cH promotes beneficial effects in T. cruzi infection in Wistar rats by modulating the secretion of IFN-γ and TNF-α with decreased inflammation in cardiac tissue. These results reinforce the importance of considering the use of homeopathy for establishing new therapeutic approaches in the management of patients with Chagas disease.