This article deals with the Fault Tolerant Control (FTC) and Fault Diagnosis (FD) for trajectory tracking in a class of nonlinear Fractional Order (FO) systems. The proposed control scheme consists of a set of FO differential equations describing a FO dynamic controller, the estimation of the unknown pseudo-states of the system and faults, the estimators that are designed have different structures, therefore, this scheme can be considered as a hybrid type. In addition, the existence and uniqueness of the solution for the controller is proved using the Banach fixed point theorem. On the other hand, it is shown that the dynamic controller, estimators and the tracking error are globally Mittag-Leffler bounded ensuring the desired trajectory tracking, in consequence a separation principle for nonlinear FO systems is presented. This FO control scheme is illustrated by considering a FO chaotic system as an example.