Born in Ruddington, near Nottingham, Brown studied at Nottingham School of Art under Andrew McCallum. From 1889 to 1892 he attended the Herkomer School of Art at Bushey. One of the earliest visiting painters to West Cornwall, during the early 1990s he worked from St Ives and Carbis Bay.

An artist giving the name Alfred BROWN exhibited two paintings, A Rough Pasture and A North-west Breeze, in the Dowdeswell Exhibition of 1890, and - if this is the same person - indicates association with the Newlyn and St Ives painters even earlier. Also at this period he began exhibiting at the RA. The Drinking Pool, purchased by Manchester in 1895, is a well known and iconic representation of his work in genre.

Popular for his atmospheric treatment of sea and coastal subjects with brooding skies, he helped bring St Ives landscape and marine painting to national prominence, being made one of the first honorary members of STISA in the 1930s.

At the Opening Exhibition of NAG in 1895 he showed a landscape entitled Wherries running down to Yarmouth. A major retrospective exhibition of his work was held in 1935 at Norwich Castle Museum, and in 1938 he was knighted. Sir John was also well-known for his Norfolk and Suffolk landscapes, although he did paint some portraits. He was a Royal Academician who deliberately resisted Modernist influences, annd was one of the signatures on the Glanville letter of November 1898 concerned about development schemes in St Ives.

His work The Raincloud, was selected for the 1988 RA Exhibition The Edwardians and After (1900-1950 paintings). He was married to the artist Mia Edwards (see separately under Mia Arnesby BROWN), who predeceased him. He died in Norfolk, his alternative home to that in St Ives for many years.