Stubbs was born in Orrington, Maine. He was the son of a shipmaster, and he was likely the master of his father's ship from 1863-73. By 1871 he painted what is likely his first ship portrait, and by 1876 he was listed as a marine painter in the Boston city directory. While in the Boston area, Stubbs shared a studio with Wesley Webber. Later, he had a studio in Charlestown where it is likely that the artist, Badger was his student.

Stubbs participated in the International Marine Exhibition of 1889, in Boston. After the death of his wife and daughter, Stubbs sank into depression. He was committed in 1894 to Worcester State Hospital, and then to the Medfield State Hospital in 1899.

Stubbs produced a large body of work and is acknowledged by the fine art community as a professional artist. Stubbs worked throughout the Eastern seaboard, creating a number of ship paintings. His paintings are held in the collections at the Mariner's Museum, the Mystic Seaport Museum, the Beverly Historical Society, the Philadelphia Marine Museum, and the Smithsonian Institution.