Church was born in Plymouth, England, the son of a saddler, and went to school locally. He taught briefly at Ashburton Grammar School. In 1887 his mother died and, with his inheritance of £100, he went to University College of Wales, Aberystwyth. With a first (London external) degree in Botany he won in 1891 a scholarship to Jesus College, Oxford, obtaining a first-class Oxford degree in botany in 1894.
