The space-set sitcom took top spot in a poll of 3,000 readers of the Radio Times.
The show, which starred ex-Coronation Street actor Craig Charles, ran on BBC Two for eight series and earned a global cult following.
The X-Files finished second, ahead of Lost, Life On Mars and Buffy The Vampire Slayer.
The magazine had banned voters from choosing Doctor Who, claiming that it was "too obvious".
Editor Gill Hudson said: "Seeing Life On Mars and Lost in the top 10 was no surprise - they are perfect examples of 'unreality TV' which is becoming one of the defining trends of the Noughties.
"But Red Dwarf at number one? That did surprise us. It hasn't even been on TV this century."