After his 1991 ordination, the diocese assigned Doerfler as parochial vicar at St. John Nepomucene Parish in Little Chute, Wisconsin, from 1991 to 1995. He went to Washington D.C. in 1995 to attend the Catholic University of America. He was awarded a Licentiate in Canon Law in 1997. After he returned to Wisconsin, Bishop Robert Joseph Banks appointed him as defender of the bond for the diocesan tribunal and parochial vicar of St. Francis Xavier Cathedral Parish.[2][5]
Bishop David Zubik named Doerfler as chancellor and vicar general in 2005. For the next year, he served as administrator of Saint Francis Xavier Cathedral. Doerfler received a Doctor of Sacred Theology in 2008 from Catholic University.[3]
In 2011, Doerfler said in a legal deposition that he destroyed records relating to possible sexual abuse crimes by diocesan priests. He stated that he destroyed the records in accordance to federal privacy laws and as part of an initiative by Bishop David L. Ricken.[6]
In 2012, Doerfler announced that self-declared transgender Catholics or Catholics in same-sex marriages could not receive baptism or communions unless they "repent".[8]