Janssen died at Meudon on 23 December 1907 and was buried at Père Lachaise Cemetery in Paris, with the name "J. Janssen" inscribed on his tomb. During his life he was made a Knight of the Legion of Honor and a Foreign Member of the Royal Society of London.
Craters on both Mars and the Moon are named in his honor. The public square in front of Meudon Observatory is named Place Jules Janssen after him. Two major prizes carry his name: the Prix Jules Janssen of the French Astronomical Society, and the Janssen Medal of the French Academy of Sciences.
Janssen named minor planet 225 Henrietta discovered by Johann Palisa, after his wife, Henrietta.