Under the leadership of Mayor and Council, the Village of Haines Junction has ten full time employees and a number of seasonal employees. The organization is governed through the Yukon Municipal Act and the bylaws and policies of the Village.

Administration is responsible for the overall administrative and financial functions of the municipality. Reporting directly to Council, the Chief Administrative Officer (CAO) provides corporate leadership to support Council's vision for the community. The CAO advises Council and makes recommendations on a variety of policy, financial, organizational, service and administrative issues. The CAO is responsible for ensuring Council direction, policies and bylaws are implemented and followed.

The municipal Treasurer provides for the overall financial management of the municipality and an Administrative Assistant provides support to all other municipal departments. The municipal office offers a wide variety of services to residents, from processing payments and various service requests, to providing information on municipal programs and services and the community in general. Administrative staff also manage the St. Elias Convention Centre.

Public Works forms the largest municipal department and delivers core services to the community, including water supply, storage, treatment and distribution and wastewater collection, treatment and discharge. Public Works maintains several kilometres of roads and streets, operates a waste management facility with a Recycle Centre and looks after the municipal cemetery and numerous trails, parks and playgrounds. The department maintains all municipal buildings including four pumphouses, one lift station, a Firehall, the Public Works shop, the Shakwak Valley Community Pool and Community Hall, the Bill Brewster Arena and Mezzanine, and the St. Elias Convention Centre.