Introduction: Drug development for Alzheimer’s disease has one of the greatest failure rates of any therapeutic field and AD is still incurable. Glycogen synthase kinase-3β is a critical enzyme implicated in the pathogenesis of AD, particularly in the hyperphosphorylation of tau protein, which leads to the formation of neurofibrillary tangles. TNF-α also plays a significant role in the pathogenesis of Alzheimer’s disease by promoting neuroinflammation, contributing to the formation of amyloid plaques and neurofibrillary tangles, impairing synaptic function, and disrupting the balance of neurotrophic factors. Phytomedicine has numerous advantages over synthetic medications, acting multiple mode of action, including being less toxic and having fewer adverse effects. Flavonoids act as a promising therapeutic target for treating Alzheimer’s disease. The present work investigates the anti-AD potentials of 35 flavonoids for the inhibition of GSK-3β and TNF-α. Methods: The physicochemical, pharmacokinetic parameters, toxicity profile and drug-likeness of the selected 35 flavonoids were predicted using SwissADME & OSIRIS data Warrier property explorer web tool. All flavonoids were selected for docking studies on GSK-3β and TNF-α protein using Autodock 4.2.1. Results: The predictions of this study suggested that among the selected 35 flavonoids, Top 3 flavonoids, such as Epicatechin gallate −10.93 kcal/mol, Fisetin −9.44 kcal/mol and Eriodictyol −8.54 kcal/mol for GSK-3β targets. TNF-α Fisetin −11.52 kcal/mol, Sterubin −10.87 kcal/mol, Biochainin A −10.69 kcal/mol were compared with standard drug donepezil. Conclusion: Therefore, these flavonoids could be utilized as possible leads for the structure-based design in the advancement of new, strong Anti-Alzheimer’s agents. However, more in vitro and in vivo analyses are required to finally confirm the outcomes of this research. © 2024 Elsevier B.V., All rights reserved.