Although born into a poor family in Bradford, Fowler gained a scholarship and in 1882 went to the Normal School of Science (later to become the Royal College of Science and now part of Imperial College, London). After graduating with a diploma in mechanics, he became assistant to Norman Lockyer at the Solar Physics Observatory in South Kensington, London. He remained there after Lockyer's retirement in 1901, being made professor of astrophysics in 1915. Finally, from 1923 to 1934 he served as Yarrow Research Professor of the Royal Society. Fowler was one of the leading figures behind the founding of the International Astronomical Union in 1919, serving as its first general secretary until 1925.

Not surprisingly Fowler worked very much in the Lockyer tradition of solar and stellar spectroscopy. He became particularly skilled in identifying difficult spectra, using his experience in producing different spectra in the laboratory. He thus detected magnesium hydride in sunspots and carbon monoxide in the tails of comets, and showed that the band spectra of cool M-type stars were due to titanium oxide. In addition, following the announcement in 1913 of the Bohr theory of the atom, Fowler was outstanding in analyzing the structure of atoms from their special characteristics.