Baines was made a deacon at Petertide 1987 (5 July) by George Hacker, Bishop of Penrith, and ordained a priest the Petertide following (3 July 1988) by David Halsey, Bishop of Carlisle, both times at Carlisle Cathedral. His first appointments were as assistant curate at St Thomas' Church, Kendal and St Catherine's Crook. He then moved to Leicester, becoming briefly associate minister of Holy Trinity, Leicester, and then Vicar of Rothley (1992-2000), during which time he was also chaplain to an adult mental health unit, before becoming Rural Dean of Goscote in 1995. In 2000, Baines became the Archdeacon of Lambeth in the Diocese of Southwark. He also oversaw the diocese's children and youth policies and was a member of the General Synod of the Church of England from 1995 until 2005.