Mountains are remarkable storehouses of global biodiversity that provide a broad range of ecosystem services underpinning billions of livelihoods. The world’s network of protected areas includes many iconic mountain landscapes. However, only ca. 19% of mountain areas globally are protected (excluding Antarctica); many mountain areas are inadequately (<30% of their total terrestrial area) or completely unprotected. To support the UN Convention on Biological Diversity’s Global Biodiversity Framework goal of protecting at least 30% of the world’s lands by 2030, we have developed a strategic decision-support tool for identifying and prioritizing which candidate mountain areas most urgently require protection. To test its efficacy, we applied the tool to the Western Himalaya Case Study Area (WHCSA). The six-step algorithm harnesses multiple datasets including mountain Key Biodiversity Areas (KBAs), World Terrestrial Ecosystems, Biodiversity Hotspots, and Red List species and ecosystems. It also makes use of other key attributes including opportunities for disaster risk reduction, climate change adaptation, developing mountain tourism, maintaining elevational gradients and natural ecological corridors, and conserving flagship species. This method resulted in nine categories of potential action—four categories for follow-up action (ranked by order of importance and priority), and five categories requiring no further immediate action (either because countries are inadequately equipped to respond to protection deficits or because their KBAs are deemed adequately protected). An area-based analysis of the WHCSA identified 33 mountain KBAs regarded as inadequately protected, which included 29 inadequately protected World Mountain Ecosystems. All 33 inadequately protected KBAs in the WHCSA are Category A1: first-priority mountain KBAs (located in the Himalaya Biodiversity Hotspot in developing countries), requiring the most urgent attention for protection and conservation. Priorities for action can be fine-filtered by regional teams with sufficient local knowledge and country-specific values to finalize lists of priority mountain areas for protection. This rapid assessment tool ensures a repeatable, unbiased, and scientifically credible method for allocating resources and priorities to safeguard the world’s most biodiverse mountain areas facing myriad threats in the Anthropocene.