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Abstract This research investigates the dynamics of nonlinear coupled hybrid systems using a modified Mittag–Leffler fractional derivative. The primary objective is to establish criteria for the existence and uniqueness of solutions through the implementation of Dhage’s hybrid fixed-point theorem. The study further analyzes the stability of the proposed model. To demonstrate the practical application of this framework, we utilize a modified Mittag–Leffler operator to model the transmission of the Ebola virus, known for its complex and diverse dynamics. The analysis is conducted using a combination of theoretical and numerical methods, including transforming the system of equations into an equivalent integral form, applying the fixed-point theorem, and developing a numerical scheme based on Lagrange’s interpolation for simulating the Ebola virus model. This study aims to enhance our understanding of Ebola virus dynamics and provide valuable insights for developing effective control strategies.