Pyrazole-chromeno[2,3-d]pyrimidine derivatives are heterocyclic compounds with diverse biological activities and potential as bioactive small molecules. Following multistep screening of eight derivatives, 8,9-dihydroxy-5-(5-methyl-3-oxo-2,3-dihydro-1H-pyrazol-4-yl)-1,5-dihydro-2H-chromeno[2,3-d]pyrimidine-2,4(3H)-dione (PCP-4) was selected for further investigation of its DNA-protective potential, based on its in vitro DNA-protective activity and in vivo antigenotoxic effects in Drosophila melanogaster. Its in vivo genotoxic and antigenotoxic effects were evaluated in the liver of male Wistar rats using the alkaline comet assay. Eight groups (n = 5/group; 8-10 weeks old; approximately 250 g) received 0.9% NaCl intraperitoneally as the negative/vehicle control, EMS alone (300 mg/kg), PCP-4 alone (1.25, 2.5, or 5 mg/kg), and PCP-4 administered 24 h after EMS treatment. Animals were sacrificed 24 h after PCP-4 administration, and liver samples were collected for DNA damage assessment. PCP-4 at 1.25 mg/kg did not significantly increase DNA damage, whereas 2.5 and 5 mg/kg produced moderate but significant increases. Total comet scores for PCP-4 alone were 23.10 ± 0.41, 40.60 ± 0.49, and 45.00 ± 1.00, respectively, compared with 166.30 ± 0.17 for EMS alone. Although higher PCP-4 doses showed intrinsic genotoxicity, the magnitude of DNA damage remained markedly lower than that produced by EMS under these conditions. Post-treatment with PCP-4 significantly reduced EMS-induced DNA damage by 82.3%, 80.1%, and 69.3%, respectively. These findings reveal a dose-dependent dual response, with pronounced antigenotoxic activity at lower doses and increased intrinsic genotoxicity at higher doses. Further studies are needed to determine the optimal protective dose of PCP-4 and elucidate the mechanisms underlying its dose-dependent effects.