The global activities of Mountain Forum are managed and coordinated by a secretariat, which is located in Kathmandu, Nepal. The secretariat is hosted by the International Centre for Integrated Mountain Development (ICIMOD), a partner organisation of the Mountain Forum. The Mountain Forum Secretariat oversees the overall coordination of the organisation's governance, fundraising, partnership building and advocacy activities, and reports directly to the Board of Directors. The secretariat is also the focal point for coordination of activities and programmes between the regional nodes, or networks. The Mountain Forum Secretariat also represents the organisation at regional and international forums to promote and advocate on issues related to sustainable mountain development.

A key task of the secretariat is also to manage the global information services, which involve among other activities, maintaining the Mountain Forum website (including the Online Library), hosting and moderating global discussion lists, maintaining the Mountain Calendar, managing e-conferences and providing technical support and training to the regional nodes.