Anthraquinone derivatives have been identified to inhibit the CK2-dependent phosphorylation of multiple key proteins implicated with apoptosis. The optimization of anthraquinones was done using density functional theory (DFT) with the B3LYP/6-311G+(d, p) basis set to determine their frontier molecular orbitals, Mulliken charges, and chemical reactivity descriptors. According to the DFT results, Chrysophanol has the smallest HOMO-LUMO gap (2.46 Kcal/mol), as well as the highest electrophilicity index and basicity. Anthraquinones were docked into the active site cavity of CK2 to evaluate their structure-based inhibitory activity. The docking simulation studies predicted that Chrysophanol has the lowest binding energy (-6.31 Kcal/mol), which is inconsistent with the DFT calculations and suggests that it could be a powerful inhibitor of CK2 comparable to its known inhibitor viz. ellagic acid, having a binding affinity of -5.05 Kcal/mol. Anthraquinones' strong binding affinity was linked to the presence of hydrogen bonds as well as various hydrophobic interactions between the ligands and the receptor's essential amino acid residues.