The music beat Red Dwarf's credit song by Howard Goodall into second place in the Total Sci-Fi website poll, while Mark Snow's X-Files instrumental came third.
Written by Ron Granier in 1963 and arranged by experimental music legend Delia Derbyshire, the Doctor Who theme was produced by combining a tape loop of a piano string with test oscillators and filters.
Editor Matt McAllister said: "The poll result proves that in addition to being one of the most popular science fiction shows ever created, Doctor Who also boasts the most iconic sci-fi theme tune.
"Grainer and Derbyshire's theme manages to convey the outlandish quality of the show and is instantly recognisable to fans throughout the world just by its opening bars."
The Doctor Who theme has been reworked a number of times, with the version on the current series arranged by Murray Gold.
By Mayer Nissim