This article proposes a method to precisely estimate the load force of magnetic lead screw (MLS)-based series elastic actuators (SEAs) in real time. The elastic transmissions of MLS-based SEAs generally comprise permanent magnets (PMs). Owing to the magnetic pole distortion and the characteristic nonlinear force of PMs, conventional force estimation methods are less accurate for MLS-based actuators than for SEAs with mechanical springs. In the proposed method, to precisely estimate force of MLSs, the nonlinear force characteristic of an MLS is modeled with a sinusoidal force model, and the magnetic force hysteresis phenomenon is predicted based on Bouc-Wen-type hysteresis equations. Moreover, a method called the relative displacement normalization method is proposed to detect the magnetic pole distortion and to compensate for the related force estimation error. In addition, the proposed method is applied to a rotary-linear (RotLin) actuator, which is a novel MLS-based linear SEA. The force estimation accuracy is experimentally evaluated by comparison with existing methods. The results demonstrate that the root-mean-square error of the proposed method is less than that of the existing polynomial model by up to 81.2%. Finally, a force controller and a static force control system is designed with the proposed model to prove its feasibility.