A novel and efficient route towards the synthesis of pyrido[2,3-d:6,5-d′]dipyrimidines 4 a–g as unexpected products through the reaction of 6-aminouracil (1) and arylidenemalononitrile or ethyl arylidenecyanoacetate in acetic acid were investigated. On the other hand, reaction of 6-aminouracil and ethyl 4-nitrobenzylidenecyanoacetate in ethanol in presence of piperidine (few drops) afforded pyrido[2,3-d]pyrimidine-6-carbonitrile 5. In addition, pyrido[2,3-d]pyrimidines 6 a–g were obtained through the reaction of 5 with different aliphatic amines in ethanol in presence of triethylamine (few drops). All reactions proceeded in good to excellent yields and the resulting compounds were characterized by different spectroscopic techniques. The antiproliferative activity of these compounds was evaluated towards HEPG-2, MCF-7 and HCT-116 cell lines. The compound 6a displayed the highest activity against the tested cell lines, followed by compound 6d, 6g and 6b, with strong affinity to bind with the active and allosteric sites of topoisomerase II, as authenticated from the molecular docking analyses.