Liquefied natural gas-fuelled ships, beginning with small-sized ships produced in the 2000s to large merchant ships, are expected to show a rapid increase in number. According to Lloyd's Register, liquefied natural gas shows great promise as fuel for new ships. In line with this trend, it is necessary to establish adequate infrastructure for liquefied natural gas fuelling systems. In the bunkering chain, bunkering shuttles retrieve fuel from the terminals to fuel liquefied natural gas-fuelled ships berthing at the ports. Many researches have dealt with the technical feasibility or the necessity of ship-to-ship bunkering considering the liquefied natural gas bunkering processes, but none has covered them at the same time. This study examines the liquefied natural gas ship-to-ship bunkering chain considering the technically feasible combinations of liquefied natural gas storage and boil off gas treatment system. The suggested method decomposes this large infrastructure problem into two steps, which are pre-processing to estimate port statistics and integer programming model. The model can represent any port as long as the port's ship statistics and their data are provided. We select three major ports with high liquefied natural gas bunkering potential as case studies to verify the proposed model.