SARS-CoV-2 posed, and continues to pose, a severe threat to life, and for fishermen in Thailand, specific multifaceted quarantine design measures have been required. In response to the SARS-CoV-2 outbreak in Trat province, a community quarantine centre was designed using boats as quarantine facilities. This study examines the implementation of boat quarantine in response to the SARS-CoV-2 pandemic within the fishermen communities in Trat province, Thailand. In-depth interviews with 45 key individuals who have been involved in the control and prevention of SARS-CoV-2 among fishermen in the fishing communities were subjected to a thematic analysis. Boat quarantine was used to separate and restrict contact between fishermen who were exposed to SARS-CoV-2, to determine whether they became sick and to prevent mass infection within the community. Using a boat as a place to self-isolate has become an effective form of quarantine for fishermen. This model has implications for the future of infectious disease control onshore, both while the pandemic continues and after the pandemic comes to an end.