This paper develops an accurate force control algorithm for series elastic actuators (SEAs) based on a novel force estimation scheme, called transmission force observer (TFOB). The proposed method is designed to improve an inferior force measurement of the SEA caused by nonlinearities of the elastic transmission and measurement noise and error of its deformation sensor. This paper first analyzes the limitation of the conventional methods for the SEA transmission force sensing and then investigates its stochastic characteristics, which indeed provide the base to render the accurate force control performance incorporated with the TFOB. In particular, a tuning parameter is introduced from holistic closed-loop system analyses in the frequency domain. This gives a guideline to attain optimum performance of the force-controlled SEA system. The proposed algorithm is experimentally verified in an actual SEA hardware setup.