Background: Alzheimer's disease (AD) is one of the most common neurological disorders occurring in older people. So far, no specific drug is available for the disease, and only palliative medicines are available for the patients. Accumulation of amyloid beta (Aβ) peptides is considered to play a crucial role in the generation of the disease. Aβ peptide is generated by the proteolysis of amyloid precursor protein by two distinct proteases β and γ-secretase. Flotillin-1 (FLOT1) directly binds to the cytoplasmic tail of β-secretase and affects the sorting and recycling of the enzyme. Increased expression of FLOT1 has been correlated with the progression of AD, while FLOT1 knockdown causes a reduction in Aβ production. Thus, FLOT1 is an attractive therapeutic target for the suppression of beta-secretase 1 (BACE-1 ). Objective: This study aims to screen the potential inhibitors against FLOT1 as therapeutics for AD. Materials and Methodology: In this work, protein–protein interactions, tertiary structure prediction, molecular docking, and molecular dynamics (MD) simulation were performed. Results: Tertiary structure prediction of FLOT1 and screening inhibitors against it helped in finding key molecules with potential therapeutic properties. Protein–protein interaction study of FLOT1 deciphered the interactors playing key role in AD. Pharmacokinetic parameters were quantified for each potential inhibitor. The results of MD simulation analysis revealed that the ZINC67911837 had better inhibitory activities with FLOT1. Conclusion: The analysis suggests that the ZINC67911837 compound could be a novel potential inhibitor of FLOT1 to modulate BACE-1 activity and used as a therapeutic agent for the treatment of AD. This study facilitates the initiation of the natural drug discovery process for the treatment of AD patients.