Flunder was born in San Francisco, California and raised in the Church of God in Christ. In 1984 she began singing and recording with Walter Hawkins and the Love Center Choir, where she was the lead singer. She was later ordained by Hawkins. In 1986, Flunder was moved to begin working with and ministering to people with HIV/AIDS in response to the epidemic of the 1980s. She founded several not-for-profit enterprises in the San Francisco Bay Area, providing services for people affected by HIV: Hazard-Ashley House, Walker House and Restoration House, through the Ark of Refuge, Inc., which later became the Y. A. Flunder Foundation. In 1991, she founded the City of Refuge under the United Church of Christ, "in order to unite a gospel ministry with a social ministry". She describes the City of Refuge UCC as an effort to "create a spiritual community that will embrace our collective cultures, faith paths, gender expressions, and sexual/affectional orientations while simultaneously freeing us from oppressive theologies that subjugate women, denigrate the LGBT community, and disconnect us from justice issues locally and globally". The Transcendence Gospel Choir at the City of Refuge is the first all-transgender choir in the United States. Flunder earned a Certificate of Ministry Studies and a Master of Arts in 1997 from the Pacific School of Religion, before earning her Doctor of Ministry degree from the San Francisco Theological Seminaryin 2001. In 2000 she founded the Fellowship of Affirming Ministries, a trans-denominational coalition of Christian churches who "desire to celebrate and proclaim the radically inclusive love of Jesus Christ", and was appointed its Presiding Bishop in 2003. Flunder identifies as a womanist and a reconciling liberation theologian. In 2005 she authored a book, Where the Edge Gathers: Building a Community of Radical Inclusion. Carlton Pearson cites her among the first religious leaders to embrace and encourage him after he was declared a heretic due to coming out in support of universal reconciliation. In 2013 she was named as a Distinguished Alumna of the Pacific School of Religion. On December 1, 2014, Flunder was a keynote speaker in the White House for World AIDS Day, where she described the harmful effects of stigma and homophobia on those living with HIV and on AIDS education in general. The following year she was a guest speaker at the American Baptist College's Garnett-Nabrit Lecture Series. Since 2015 Flunder has been a member of the board of trustees of the Starr King School for the Ministry and also served as a member of the Presidential Advisory Council on HIV/AIDS. Flunder's spouse is Shirley Miller, the cousin of Walter Hawkins; they have been committed partners since the mid-1980s.
