Mountain ecosystems across South Asia are facing huge pressure and are threatened by different drivers of loss. Red List of Ecosystems, to assess risks and ecosystem health, offers an exciting prospect to address complex challenges faced by ecosystems. This opinion is an outcome of the brainstorming organized to mark the International Mountain Day in December 2020, followed by further discussions among key stakeholders for initiating the Red List of Ecosystem (RLE) assessment in the region. As an initial endeavor, we have explored the evidence available to be integrated with the basic RLE requirements to undertake the ecosystem health assessment for mountain ecosystems in South Asia. We argue that the existing data gaps and insufficient understanding of the RLE process are a key-barriers to initiating ecosystem health assessment for supporting and contributing to knowledge-based conservation, governance, livelihood, land use, and macroeconomic planning. The RLE-based planning should be expanded and implemented for diverse ecosystems by enhancing transboundary cooperation, research collaboration, co-production of knowledge, and involving local communities. This opinion paper is an effort to facilitate, encourage and enhance discussions among wider stakeholders for developing a multidisciplinary and transdisciplinary network of experts in the region for undertaking large scale RLE assessment for different mountain ecosystems that are threatened by an array of drivers of biodiversity and ecosystem services loss. This can guide strategic conservation efforts to halt and reverse the losses by community supported landscape restoration programmes.