Donepezil is an acetylcholinesterase inhibitor (AChEI) in use to treat symptomatic patients of mild to moderate Alzheimer’s disease (AD). Ferritin is an iron protein associated with storage and sequestration of excess ferrous iron in a way maintaining proper function of cellular processes and plays a key role in AD since steady-state dysregulation of metal ion metabolism in vivo is associated with AD pathology. In lieu of therapeutics importance of ferritin and donepezil in AD, this study aims at investigating the binding between these two employing molecular docking and molecular dynamics (MD) simulation. In this study, we performed structure-based docking of donepezil with human Ferritin. Primarily, the top pose based on the binding affinity was selected and then interaction analysis was carried out to find the stable pose. Structural annotations by docking analysis were further accompanied by all-atom MD simulation for 100 ns followed by principal component and free energy landscape analyses to investigate the conformational changes, stability, and interaction mechanism of ferritin with donepezil. MD simulation suggested that the binding of donepezil stabilizes the ferritin structure and leads to fewer conformational changes. This study gives an insight at the atomistic level into the interaction between donepezil and ferritin thereby aiding in understanding the activity and mechanism of protein and drug binding. The study is clinically significant as iron participates in the occurrence of AD. © 2020 Informa UK Limited, trading as Taylor & Francis Group.