The aim of this work was to solve the structure of the enzyme dihydrofolate reductase from Toxoplasma gondii (TgondiiDHFR) as a target for drug discovery on account of recent reports of parasite's growing resistance to pyrimethamine (CP6), which is the reference pharmaceutical used to treat toxoplasmosis and malaria. The tertiary structure of the protein bonded to NADP(+) and CP6 was solved by homology modeling. The best output model was subjected to conjugate gradient minimization and the comparison with templates shows important replacements at the inhibitor's binding site allowing selective drug design. CP6 redocking in TgondiiDHFR shows a ΔGbinding of -8.66 kcal mol(-1), higher than those found for templates Plasmodium vivax (-9.01) and P. falciparum (-8.99). Virtual screening of ligands similar to CP6 was performed using the ZINC database and docking procedures were carried out. The result indicates the substances ZINC14966516, ZINC13685962, ZINC13685929 and ZINC13686062 with a ΔGbinding of -10.57, -10.09, -9.87, and -9.76 kcal mol(-1), respectively, as the best choices. NPT molecular dynamics with the complexes indicates that they remained stable along the 10 ns simulation and they dock to TgondiiDHFR by salt bridges to the Asp 30 and to nine other residues in the contact region, which makes it more difficult for single mutations to acquire resistance. The contact frequency of protein residues with ligands suggests plausible explanations for site-directed mutagenesis studies regarding CP6 resistance described previously in the literature. All results indicate that the new ligands could be tested as pyrimethamine substitutes in the treatment of toxoplasmosis, in addition to other protozoonosis diseases.