The heart of UNITY is its affiliated youth councils, which are sponsored by tribes, Alaska Native villages, high schools, colleges, urban centers, and others. Youth Councils engage in annual projects in four areas – cultural preservation, environmental awareness, healthy lifestyles, and community service. UNITY has a growing number of affiliated youth councils, which currently stands at 320 in operation in 36 states. UNITY is the only organization to have a formal network of youth councils.

Members of each UNITY-affiliated youth council appoint two individuals (one young woman, one young man) to serve as their representatives on the National UNITY Council (NUC). Native youth throughout the United States, who are UNITY affiliates, elect individuals to serve as Area Representatives on the National UNITY Council Executive Committee. The ten geographical areas are as follows: Great Plains, Midwest, Northeast, Northwest, Pacific, Rocky Mountain, Southeast, Southern Plains, Southwest, and Western. Two youth (one young man, one young woman) are elected by the NUC membership each year to serve as National UNITY Council Co-Presidents.