This paper studies the throughput performance of a two-way energy harvesting relaying system. Network Coding and Energy Harvesting are promising techniques that can improve the transmission efficiency and the energy efficiency of wireless systems, respectively. In particular, we focus on the energy harvesting system with the power splitting-based relaying (PSR) protocol, and consider both the amplify-and-forward (AF) relaying and decode-and-forward (DF) relaying methods for the network coding. We successfully derive the expressions for both the outage probability and the system throughput for each case. It can be shown that DF relaying system outperforms AF relaying system in terms of both the outage probability and the throughput. Furthermore, simulations show that the throughput gain brought by network coding highly depends on the signal-to-noise ratio (SNR) at the receiver. The throughput gain can be up to 33% in the high SNR region.