This paper presents the modeling and control of an opposed piston (OP) engine in a novel hybrid architecture. The OP engine was selected for this work due to the inherent thermody-namic benefits and the balanced nature of the engine. The typical geartrain required on an OP engine was exchanged for two electric motors, significantly reducing friction and decoupling the crankshafts. By using the motors to control the crankshaft motion profiles, this configuration introduces capabilities to dynamically vary compression ratio, combustion volume, and scavenging dynamics. To realize these opportunities, a model of the system capturing the instantaneous engine dynamics is essential along with methodology to regulate the crankshaft’s rotational dynamics utilizing the electric motors. The modeling presented here couples a 1D model capturing the gas exchange process during scavenging and a 0D model of the crankshaft dynamics and the heat release profile due to combustion. With the use of this model, a linear quadratic controller with reference feedforward was designed to track the crankshaft motion trajectory. Experimental results are used to validate the model and controller performance. These results highlight the sensitivity to model uncertainty at points with high cylinder pressure, leading to large differences in control input near minimum volume. The proposed controller is, however, still able to maintain tracking error for crankshaft position below ± 1 degree.