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In this paper we introduce the (k, s)-Hilfer-Prabhakar fractional derivative and discuss its properties. We find the generalized Laplace transform of this newly proposed operator. As an application, we develop the generalized fractional model of the free-electron laser equation, the generalized time-fractional heat equation, and the generalized fractional kinetic equation using the (k, s)-Hilfer-Prabhakar derivative.