The tourism sector is the economic sector hardest hit during the Covid-19 pandemic. A breakthrough is needed in line with health protocols to maintain physical and social distance. Tourism on the outermost islands is an alternative solution. As the largest archipelagic country globally, Indonesia has the potential for the outermost islands that can be used as tourist destinations. A breakthrough policy is needed in the management of ecotourism in the outermost islands related to the limited capability of the Government, such as the high costs for transportation and logistics arrangements in the outermost islands. Tourism in the outermost islands must be directed towards premium tourism. Its market share is middle to upper-class tourists who want a new atmosphere and challenges and are willing to pay quite a lot of money. This study presents a management model that divides each government agency’s duties in managing ecotourism in the outermost islands with a premium scheme and the National Border Management Agency being the operator. The model is expected to encourage the formulation of targeted policies for the management of the outermost islands, including the presence of cruise ships.