The National Elk Refuge borders the Bridger-Teton National Forest, with several public refuge roads and trails leading to forest lands. One of the key projects the refuge coordinates with the Bridger-Teton National Forest is the implementation of winter closures to protect wildlife.

The refuge's partnership with the Grand Teton Association is unique because not only does the association work to increase public understanding and enjoyment of the National Elk Refuge, but it provides funding critical to refuge interpretive, educational, and research projects. 

Another of the refuge's boundaries is shared with Grand Teton National Park. Park and refuge managers collaborate on many wildlife issues, including the implementation of the Bison and Elk Management Plan that provides a 15-year strategy for managing the two herds.

The Greater Yellowstone Coordinating Committee was formed to allow representatives from the National Park Service, US Forest Service, US Fish and Wildlife Service, and the Bureau of Land Management to pursue opportunities of mutual cooperation and coordination in the management of core federal lands in the Greater Yellowstone area.

The Jackson District Boy Scouts have a unique partnership with the National Elk Refuge, assisting with collecting and auctioning elk antlers from the refuge. The local Scouts and leaders contribute several thousand hours of their time collecting and preparing the antlers for the annual antler auction.

The multi-use pathway on the National Elk Refuge is part of a larger network of trails constructed and maintained by Jackson Hole Community Pathways of Teton County. 

The refuge supports several Jackson Hole Conservation Alliance projects, including the "Don't Poach the Powder" educational campaign that raises awareness of the threats posed to wildlife survival when humans encroach on crucial winter habitat, and the "Wild Neighborhoods" program encouraging people to live appropriately amid the wildlife and wild spaces of the Jackson Hole valley. 

The refuge has donated both funding and recorded public service announcements in support of the Wildlife Foundation's "Give Wildlife a Brake" campaign, a program designed to reduce wildlife-vehicle collisions. 

Additionally, the refuge is part of the "Nature Mapping Jackson Hole" working group that trains volunteer citizen scientists to record wildlife sightings in a comprehensive database for use in land use planning and wildlife-related data needs. Fence removal projects on the National Elk Refuge supported the Foundation's program to remove obsolete and dilapidated fences, allowing wildlife to move more freely throughout the valley and eliminating hazards that may cause entanglement.

The refuge works closely with Teton County Weed & Pest to control the establishment and spread of noxious weeds on the landscape. Each year, refuge staff participates in the Gros Ventre Spray Days event, a multi-agency effort to control weeds along the Gros Ventre River riparian corridor.

The National Elk Refuge is part of the Teton Interagency Fire Program, which includes partnerships with the Bridger-Teton National Forest, Grand Teton National Park, and Jackson Hole Fire/EMS.

The Wyoming Game & Fish Department is a key partner in wildlife management. The state organization coordinates with refuge staff on  decisions related to refuge hunting seasons, monitoring forage conditions and determining when to initiate winter supplemental feeding for elk and bison, and testing wildlife for disease.