The church maintains a fund known as The Second Unitarian Church of Omaha Endowment Fund. The purpose of the Endowment Fund is to enhance the mission of Second Unitarian Church and to promote Unitarian Universalist principles in the community independently from the annual operating budget. No distributions from the fund will be made until it surpasses $250,000.

The Endowment Fund Committee (EFC) is the custodian of the Endowment Fund. The EFC consists of three members, all of whom are voting members of the Second Unitarian Church of Omaha for a minimum of one year. One member will be elected each year at the Annual Meeting. The term of each member is three years. No member of the EFC shall serve more than two consecutive three-year terms. The minister, the chairperson of the Board of Trustees, and a representative from the Finance Committee are advisory, non-voting members of the EFC.