Phase separation has been proven to be beneficial to air-cooled parallel flow microchannel condensers for air conditioning systems. The inlet to the condenser with phase separation is at the middle of the condenser height. After the first pass, in the vertical second header of the condenser, refrigerant vapor separates from liquid mainly due to gravitational effects. In ideal case, vapor should go to the top exit and liquid to the bottom exit, resulting in increased heat transfer. Due to interaction between vapor and liquid, separation is not perfect, expressed through the separation efficiency. This paper presents a parametric study of phase separation efficiency in the intermediate headers, with the target to improve separation efficiency. Header prototypes which have two exits are made with transparent polyvinyl chloride (PVC) to simulate the real header and provide visual access. Using R-134a as a baseline, the measurement of separation efficiency and its general trend will be shown first. The experimental results are compared to the simulation of a mechanistic model based on flow regime and force balance analysis. Inlet mass flux in simulation is controlled at 87–311 kg · m−2 · s−1 and inlet quality at 0.05–0.25. The observed flow patterns in header are compared with the modeling results. Then, the header diameter is increased, which effectively improves the separation efficiency due to reduction of vapor velocity in header. Finally, R245fa and R32 are modeled in comparison with R-134a to discuss the effect of fluid properties on separation efficiency.