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Out-of-universe Edit

Moffat on Doctor Who's Real Name - Comic-Con 2012, SDCC

Moffat on Doctor Who's Real Name - Comic-Con 2012, SDCC

Editor's Note: Needs expansion to cover pre-revival out-of-universe material

Nobody knows the Doctor's name, because none of the writers have ever invented one for him. And they likely never will. Current show-runner Steven Moffat explained that any name they give him now would be anticlimactic, and take away from the mystery of the show without adding anything new, and many of his predecessors (and equivalents in other media, like the novel range editors) said the same thing (Moffat illustrates the ridiculousness of assigning a name to the Doctor in Doctor Who Magazine #475 where he jokingly says the Doctor's real name is Mildred). We do know that he calls himself "The Doctor", and sometimes "Theta Sigma" (an old Academy nickname, and possibly later an undercover name), and other aliases like "John Smith", but none of those are his real name.

Moffat has jokingly suggested that he knows the real name, such as at the 2012 San Diego Comic Con, but this is not to be taken seriously given he also claimed at the same event that William Hartnell told him the character's name when he was all of one year old.

In-universe Edit

In-universe, of course, the Doctor knows his name, and there may be a few others.

In the past, there were many Time Lords who knew it and, as we learned from "The Day of the Doctor" & "The Time of the Doctor", at least one surviving Time Lord on Gallifrey must still know it (otherwise, the Doctor's name couldn't be used to identify the correct universe to which to return the planet). Plus, a few of his companions knew it, but they may all be either dead or unable to remember it. (We know he told Peri Brown ["Slipback" (audio story)], but she couldn't pronounce it and could only remember the first syllable; in the novels he told Sam Jones, but she's dead; Donna likely got the knowledge while she was Doctor-Donna, but can no longer access any of those memories without her brain burning out. Clara becomes aware of it in "Journey to the Centre of the TARDIS" but loses the knowledge soon after.) It should be noted that possibly Clara actually does know his name, as she even masquerades as the Doctor briefly in "Death in Heaven".

In fact, the only people we know of that know the Doctor's name are the Doctor himself and River Song (she tells the Doctor his name in "Silence in the Library" and uses his real name to open the TARDIS in "The Name of the Doctor"). And it seems likely they're the only two, period—one of the New Series Adventures novels confirms that before he told River, nobody alive knew his name, but even if you ignore the novels, it's hard to think of anyone else who'd be likely to have that secret.

And his name is a very big secret. There have been hints going back to the classic series (e.g., Lady Peinforte in "Silver Nemesis"), but series 6 made it as blatant as possible: The First and Oldest Question, the question that's the core of the Silence's beliefs, the question that should never be answered, is "Doctor Who?" (because the answer would identify the universe to which Gallifrey belongs, allowing the planet to return, possibly re-igniting the Last Great Time War).

It may be worth noting that the Doctor accidentally says his name in "Return of the Living Dad" (Virgin New Adventures novel #53), after he has been drugged or something. Unfortunately, author Kate Orman unsportingly doesn't tell the reader what he actually says, although the character to whom he is speaking comments that it would be difficult to address an envelope with it (a reference to long Gallifreyan names such as Romanadvoratrelundar)

Nicknames & Pseudonyms Edit

While the Doctor's original name is unknown, he has been known to use many alternative names for himself over the course of history.

The Doctor
As already mentioned, "the Doctor" is itself a pseudonym. It's a name he chose for himself as a promise to be "never cruel or cowardly", "never give up, never give in" ("The Day of the Doctor").
John Smith
Most famously, he's used the pseudonym "John Smith" and variations thereof in almost every incarnation since his first ("The Vampires of Venice", "The Witch Hunters" (novel)).
Doctor Who
As well as being the name of the show, this and its variations are another long-running alias for the Doctor. This exact name for him has only been used in two instances on screen. The first is when when WOTAN referred to him as such in "The War Machines", and the second was in "World Enough and Time" when Missy explicitly says that "Doctor Who" is the Doctor's real name, although it is strongly implied that she was joking. He has also used variants of this alias, once going by the name "Doktor von Wer" (German for "Doctor of Who") in "The Highlanders" and signing his name "Dr W" in "The Underwater Menace". It was also used in many of the comics and novelisations in the 1960s an early 1970s, but primarily in non-dialog text.
Another example is in "Rose", with Clive's website asking "Who is Doctor Who?". This is only briefly glimpsed in the episode itself, but if you go to the real life official BBC version of the website, he is referred to as Doctor Who throughout, notably in the privacy policy and sightings sections (it should be noted, though, that, while the website does have some serious parts - including what appear to be the Ninth Doctor's otherwise undepicted first words, a great deal of it is toungue-in-cheek - particularly the more [intentionally] poorly written 'sightings').
While the evidence given above does give some credit to the view that "Doctor Who" is the Doctor's actual, original name rather than just another alias, it should be noted that there is a lot of evidence against this fact. This includes amongst others the fact the use of the phrase "Doctor Who" did not bring Gallifrey back through the cracks in Series 7, which it should have done if it were the Doctor's actual name ("The Bells of Saint John", "The Time of the Doctor"), and the fact that Peri both knew the Doctor's real name and found it unpronounceable ("Slipback" (audio story)), a category which "Doctor Who" doesn't seem to fit.
Theta Sigma
Theta Sigma, sometimes shortened to Thete, was the Doctor's nickname at the Academy. ("The Armageddon Factor", "The Happiness Patrol")
The Oncoming Storm
This was one of the names used for the Doctor by the Daleks in their legends and was often embraced by the Doctor himself when he wanted to seem impressive. ("The Parting of the Ways", "The Lodger", "The Day of the Doctor")
The Doctor's granddaughter, Susan, referred to him as "Grandfather". ("An Unearthly Child" etc) Bill also called the Doctor this when she pretended the Doctor was her grandfather. ("Knock Knock")
The Professor
This was Ace's nickname for the Doctor, which she use despite the Doctor correcting her. ("Dragonfire" etc)