A set of new derivatives of 4,8-disubstituted pyrimido [5,4-d]pyrimidines were efficiently synthesized and in vitro evaluated against Trypanosoma brucei and Leishmania infantum promastigotes and intramacrophage amastigotes. The in vitro cytotoxicity was determined using the THP-1 cell line, and early in vitro ADME-Tox was carried out using in vitro assays for cytotoxicity (A549 and HEK293 cell lines) and CYP3A4 and hERG cardiotoxicity liabilities. All the new compounds were active against T. brucei (0.11 μM ≤ IC 50 ≤ 8.72 μM; 1 ≤ selectivity index (SI) ≤ 877), but only eight were active against L. infantum promastigotes (0.20 μM ≤ IC 50 ≤ 14.88 μM; 1 ≤ SI < 502) with three also active against L. infantum intramacrophage amastigotes (3.00 μM ≤ IC 50 ≤ 8.51 μM). Compounds 4a, 4c, and 4n were identified as the hit compounds to further develop as antitrypanosomal and antileishmanial agents.