This paper considers a three-way wireless communication system employing physical layer network coding (PNC), where each user desires to transmit independent data to the other users via relay. However, one difficulty with this system is that the performance is limited by the worst channel. To overcome this problem, we adopt a scheduling system. Since channel characteristics vary over time in wireless communications, a scheduling technique employing network coding where users are selected based on the instantaneous signal-to-noise ratio was proposed for the broadcast channel (BC) phase. In this paper, we extend the scheduling technique to the multiple access channel phase as well as the BC phase. We propose two criteria for selecting users based on the channel norm and the minimum distance criterion. Also, an efficient method to compute the minimum distance is introduced. The proposed scheduling for PNC provides a significant improvement over the conventional scheme.