This paper discusses low level control of the humanoid UT-Theta which has been been developed at the University of Tokyo. This innovative humanoid walking robot is equipped with knee joint switchable between active and passive operation mode using a backlash clutch. A nonlinear, time optimal, hybrid controller for this knee joint is presented. The controller avoids discontinuities in the commanded trajectories thus ensuring smooth trajectory following. Relevance to practical application is shown in hardware experiments.