Fowler established a busy practice, working on many railway schemes across the country. He became chief engineer for the Manchester, Sheffield and Lincolnshire Railway and was engineer of the East Lincolnshire Railway, the Oxford, Worcester and Wolverhampton Railway and the Severn Valley Railway. In 1853, he became chief engineer of the Metropolitan Railway in London, the world's first underground railway. Constructed in shallow "cut-and-cover" trenches beneath roads, the line opened between Paddington and Farringdon in 1863. Fowler was also engineer for the associated District Railway and the Hammersmith and City Railway. Today these railways form the majority of the London Underground's Circle line. For his work on the Metropolitan Railway Fowler was paid the great sum of £152,000 (£ today), with £157,000 (£ today), from the District Railway. Although some of this would have been passed on to staff and contractors, Sir Edward Watkin, chairman of the Metropolitan Railway from 1872, complained that "No engineer in the world was so highly paid."