Hybrid powertrain systems have been developed to improve the fuel efficiency of internal combustion engines. In the case of a parallel hybrid powertrain system, an engine and a motor are directly coupled. Because of the hardware configuration of the parallel hybrid system, friction and the pumping losses of internal combustion engines always exists. Such losses are the primary factors that result in the deterioration of fuel efficiency in the parallel-type hybrid powertrain system. In particular, the engine operates as a power consumption device during the fuel-cut condition. In order to improve the fuel efficiency for the parallel-type hybrid system, cylinder deactivation (CDA) technology was developed. Cylinder deactivation technology can improve fuel efficiency by reducing pumping losses during the fuel-cut driving condition. In a CDA engine, there are two operating modes: a CDA mode and an SI mode according to the vehicle operating condition. However, during the mode change from CDA to SI, a serious fluctuation of the air-fuel ratio can occur without adequate control. In this study, an air-fuel ratio control algorithm during the mode transition from CDA to SI was proposed. The control algorithm was developed based on the mean value CDA engine model. Finally, the performance of the control algorithm was validated by various engine experiments.