We assessed the association between voluntary polymerase chain reaction testing of travellers and reported infection rates in the Ogasawara Islands compared with those in several other Tokyo islands. The implementation of polymerase chain reaction testing over a 2-year period was evaluated. Between September 2020 and September 2022, 38,943 of 45,900 travellers to the Ogasawara Islands underwent pre-travel polymerase chain reaction testing, with a notable increase in uptake during states of emergency. Ogasawara reported 385 positive coronavirus disease 2019 cases, with no hospitalizations or severe cases among residents, in contrast to the higher infection and hospitalization rates in Tokyo. Pre-boarding polymerase chain reaction tests were associated with lower reported infection rates in this island setting. These findings suggest that combining pre-travel testing with local mitigation measures, including case isolation systems, may help safeguard the communities of small, geographically isolated islands. These results may inform public health preparedness and response strategies for future infectious disease outbreaks.