Pilgrim Congregational UCC follows a congregational style of governance, which means that major decisions are made by the membership of the congregation. The pastor serves as spiritual leader and chief administrator of the church.

The leadership of the church consists of a church council, boards, and committees, which is elected at an Annual Meeting in January. The roles of the council, boards, and committees are outlined in the church constitution.

The Church Council is responsible for coordination of church programs, fundraising efforts, and provides general supervision. The Council is made up of representatives from the boards, three at-large members, and a church clerk. One of the at-large members serves as chair of council and moderator of the congregation, while the pastor serves as vice chair.

The Board of Diaconate is responsible for worship, hospitality, evangelism, and keeping track of membership.

The Board of Faith Formation and Discipleship is responsible for programs related to faith formation programs, community outreach and service, support of other organizations and causes, and guiding Pilgrim in the areas of peace, justice, and care of creation.

The Board of Trustees is responsible for oversight of the operating budget and endowment, maintenance of the building and space usage, insurance, and personnel. The Trustees appoint a Church Treasurer.

Each board has six members who can serve two three-year terms.