In this paper, we propose a joint transceiver design for single-carrier frequency-domain equalization (SC-FDE) based multiple-input multiple-output (MIMO) relay systems. To this end, we first derive the optimal minimum mean-squared error linear and decision-feedback frequency-domain equalization filters at the destination along with the corresponding error covariance matrices at the output of the equalizer. Subsequently, we formulate the source and relay precoding matrix design problem as the minimization of a family of Schur-convex and Schur-concave functions of the mean-squared errors at the output of the equalizer under separate power constraints for the source and the relay. By exploiting properties of the error covariance matrix and results from majorization theory, we derive the optimal structures of the source and relay precoding matrices, which allows us to transform the matrix optimization problem into a scalar power optimization problem. Adopting a high signal-to-noise ratio approximation for the objective function, we obtain the global optimal solution for the power allocation variables. Simulation results illustrate the excellent performance of the proposed system and its superiority compared to conventional orthogonal frequency-division multiplexing based MIMO relay systems.