Drug latentiation is a process of modifying a drug molecule structurally to improve its binding affinity as well as increasing the drug-receptor interactions and potentiate its therapeutic potential. In the quest for discovering more potent epidermal growth factor receptor (EGFR) inhibitors, gefitinib-based derivatives were designed by simple structural modification at the secondary amine of gefitinib by N-alkylation. Three gefitinib derivatives (gefitinib-NB, -NP, and -NIP) were synthesized by N-alkylation and phase transfer catalysis. Structural characterization, physicochemical parameters such as solubility, log P, and p K a were determined. Molecular docking studies were carried out to investigate the binding interactions at the active site. Further drug-bovine serum albumin (BSA) protein and drug-calf thymus (CT) DNA interactions were performed to understand the pharmacokinetics of the synthesized derivatives. All the compounds were screened for preliminary in vitro cytotoxic activity against A549, A431 lung, and MDA-MB-231 breast cancer cell lines by MTT assay. The gefitinib-NP and gefitinib-NB derivatives exhibited strong cytotoxic activity compared with gefitinib. They also showed higher drug-BSA and drug-DNA interactions. Molecular docking studies showed the orientation and binding interactions with the EGFR as well as with BSA and CT DNA. The results establish a strong correlation between the experimental and molecular docking studies. EGFR inhibition studies were also carried out for the derivatives and we identified the NP derivative of gefitinib as a potential lead compound. The gefitinib-based derivatives reported herein are cytotoxic agents and can be tested for further pharmacokinetic profiles and toxicity studies which might be helpful for designing more potent gefitinib-based derivatives in the future.