The fractional Schrödinger equation (FSE) on the real line arises in a broad range of physical settings and their numerical simulation is challenging due to the nonlocal nature and the power law decay of the solution at infinity. In this paper, we propose a new spectral discretization scheme for the FSE in space based upon Malmquist–Takenaka functions. We show that this new discretization scheme achieves much better performance than existing discretization schemes in the case where the underlying FSE involves the square root of the Laplacian, while in other cases it also exhibits comparable performance. Numerical experiments are provided to illustrate the effectiveness of the proposed method.