In 1846 Bodley became a pupil in the office of George Gilbert Scott, who was a relation by marriage. Scott was then as the beginning of his career as the most prolific and eminent British Gothic-revival architect. Although Bodley found Scott's approach to design unimaginative, he learned a great deal from his technical expertise and deep knowledge of medieval architecture. He also made some important friendships in the office, notably with the brilliant young architect George Edmund Street.

Bodley's first commissions date from 1852. The buildings he designed in his first decade in practice were intended to 'develop' Gothic into a new, modern style. They blend French and Italian sources and look back to an earlier, more austere form of Gothic than Scott's. This consciously paralleled the Pre-Raphaelites' attempt to reinvigorate modern art by returning to the ideals of the early Italian painters. Bodley's determination to give the Pre-Raphaelite artists opportunities to decorate his churches was realised in his pioneering use of William Morris's firm, founded in 1861.