In this paper, we applied a fractional multi-step differential transformed method, which is a generalization of the multi-step differential transformed method, to find approximate solutions to one of the most important epidemiology and mathematical ecology, fractional stochastic SIS epidemic model with imperfect vaccination, subject to appropriate initial conditions. The fractional derivatives are described in the Caputo sense. Numerical results coupled with graphical representations indicate that the proposed method is robust and precise which can give new interpretations for various types of dynamical systems. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.