Ecotourism provides simultaneous benefits for conserving nature, respecting local cultures, and benefitting local communities. Generally, protected areas provide a suitable physical setting for ecotourism development, but they have various limitations in biodiversity conservation as well as the promotion of ecotourism. This study aims to assess the constraints in developing ecotourism in protected areas. Chundikulam, Delft National Park, and Nagar Kovil Nature Reserve were declared as protected areas after the end of the last thirty years of ethnic unrest in Jaffna district, Sri Lanka. The methodology includes qualitative interviews with key stakeholders such as government officers, managers of the private sector, and workers in non-governmental organizations. Twenty respondents were selected, and semi-structured interviews and focus group discussions were employed to collect qualitative data. The collected information was thematically analyzed. The categorized themes include awareness of the protected areas and ecotourism principles, biodiversity conservation, public participation, the livelihood of the local community, utilization of resources, and coordination among stakeholders. The results revealed that the respective government departments failed to gain support from stakeholders during the process of protected area boundary demarcation, as most people were against the initiative. As a result, this has become a barrier to gaining stakeholders' support which stifled ecotourism development. This study suggests that proper engagement and training for stakeholders should be a pre-requisite for protected area management and ecotourism development, implementation of co-management activities, re-demarcation of boundaries of protected areas, and creation of buffer zones within an ecotourism park to develop ecotourism effectively.