wilmer began his ordained ministry by serving at st. anne's parish in albermarle, virginia, from 1834-1838. the following year he served as the chaplain at his alma mater, the university of virginia. in 1839, he was appointed chaplain in the united states army. he resigned from the army in 1843 to take charge of hungars parish in northampton county, virginia. after that he served as rector of st. paul's episcopal church in goochland county, virginia, until 1848, when he became rector of st. mark's episcopal church in philadelphia, pennsylvania. he served there until the breakout of the civil war in 1861, when he retired to his estate in virginia.