In this study, the occurrence of antibodies to Toxoplasma gondii in Brazilian agouti (Dasyprocta aguti) was compared by modified agglutination test (MAT) and indirect fluorescent antibody test (IFAT) using anti-capybara conjugate. Sera from 109 animals were tested using MAT (1:25 cut-off) and IFAT (1:16 cut-off); 19% were positive by MAT, and 18% were positive by IFAT. Overall, the 17 IFAT-positive samples were also positive for MAT. The four positive MAT samples with a titer ≤200 were IFAT negative. All negative samples obtained by MAT matched with the results of the IFAT. Comparing both tests, and considering MAT as the gold standard, the sensitivity of IFAT was 81%, the specificity was 100%, the accuracy was 97%, the positive predictive value (PPV) was 100%, and the negative predictive value 96%. The kappa value agreement was 87.3% (75.1–99.6%). The anti-capybara conjugate can be successfully used to perform IFAT in Brazilian agouti with maximum specificity and PPV.