A series of Schiff bases of 4-amino-1,2-naphthoquinone were synthesized, purified, characterized, and evaluated for cytotoxicity against a panel of human cancer cell lines (Hep-G2, MG-63, and MCF-7). The cells were dosed with these Schiff bases at varying concentrations, and cell viability was measured by a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Significant anticancer activities were observed in vitro for some members of the series and compounds 4-(3,4,5-trimethoxybenzylideneamino)naphthalene-1,2-dione (S10) as well as 4-(4-hydroxy-3-methoxybenzylideneamino)naphthalene-1,2-dione (S13) are active cytotoxic agents against different cancer cell lines with IC50 values in the range of 5.91–9.98 lM. The structures of synthesized compounds were established by spectroscopic (FT-IR, 1 H NMR, 13C NMR) and elemental analysis. To study the molecular basis of interaction and affinity of binding of the target molecules, all the compounds were docked into the ATPase domain of Topoisomerase-II (TP-II) by using Schro¨dinger molecular modeling software package. Docking experiments showed a good correlation between their predicted glide scores and the observed IC50 values of synthesized compounds. Structure– activity relationships indicated that presence of electron donating groups on phenyl ring of Schiff bases enhances the activity but Schiff base with electron withdrawing substituents on phenyl ring shows diminished activity.