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In terms of series within the franchise, Doctor Who has crossed over with Thr Sarah Jane Adventures in "School Reunion" (a 'backdoor pilot' for SJA), "The Wedding of Sarah Jane Smith" "The Stolen Earth", "Journey's End", "The End of Time" and "Death of the Doctor" (plus flashbacks). Characters from The Sarah Jane Adventures and Torchwood crossed over on numerous occasions. The only three-way crossovers occurred in the episodes "The Stolen Earth", "Journey's End" and "The End of Time" . The Doctor has been mentioned in Torchwood and the episode "End of Days" leads directly into "Utopia", but the Doctor has to date never appeared in that spin-off, even in flashback. Torchwood has, however, appeared in various Doctor Who episodes, "Tooth and Claw", "Army of Ghosts", "Doomsday" (all three aired before Torchwood started), "End of Days" (Torchwood story) "Utopia", "The Sound of Drums", "Last of the Time Lords", "The Stolen Earth", "Journey's End", "The End of Time". K9 from Doctor Who obviously appeared in every episode of his own shows, 'K9', and K9 and Company. Also, the Doctor appears in "For Tonight We Might Die" Characters from EastEnders appeared in the 30th anniversary minisode "Dimensions in Time", and Matt Smith played the Doctor in a comedy skit recorded for the 2013 Comic Relief appeal in which the Doctor meets the cast of Call the Midwife. Numerous comedy series have spoofed Doctor Who, however, the TARDIS and the Doctor do make a cameo appearance (seen from the distance and unidentified) in an episode of the sitcom Chelmsford 123. There was also a comic strip where Doctor Who crossed over with Star Trek: The Next Generation, as well as TOS. The EU has had fairly frequent crossovers with both TV and other mediums, for example with Sherlock Holmes in "All-Consuming Fire" (novel)/"All-Consuming Fire" (audio story), the Cthulhu mythos in "White Darkness" (novel), "The Nameless City" (short story), and others, and SJA in "The Wedding of Sarah Jane Smith", and "The Temptation of Sarah Jane Smith".

Behind the scenes, it is known that Russell T Davies explored the possibility of a crossover between Doctor Who and Star Trek: Enterprise in 2004-2005, but the latter series was cancelled before this went any further.

"Comic Relief 2007" is a (spoof) crossover with The Catherine Tate Show.