In this work, we investigate the asymptotic stability analysis for two classes of nonlinear fractional systems with the regularized Prabhakar derivative. The stability analysis of the neutral and integro-differential nonlinear fractional systems are studied by assessing the eigenvalues of associated matrix and applying conditions on the nonlinear part of these types of systems. We use a numerical method to solve the fractional differential equations with the regularized Prabhakar fractional derivative. We further present the numerical simulations on several test cases to examine and reveal the complex dynamics of the analytical obtained results.