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Often referred to as one of the best, if not the best, writers on Doctor Who (1963), his period as script editor on the series, with Philip Hinchcliffe as producer, is also considered by many to be the high point of the entire series. In a poll for Doctor Who (1963) Magazine in 1998, three of the stories voted into the top five were written by Holmes, with the other two being from his period as script editor. In fan site Outpost Gallifrey's 40th Anniversary Poll, five of the serials from his time as script editor were voted by fans into the top ten. Four of the stories voted into the top ten were written by Holmes, including one he wrote under the pseudonym of Stephen Harris. The top three were all written by Holmes.

His work on Doctor Who (1963) was the subject of the documentary Behind the Sofa: Robert Holmes and Doctor Who (2003).

Both Russell T. Davies and Steven Moffat cited Holmes' writing as an influence on their work on Doctor Who (2005). They both cited Holmes' story "The Ark in Space" as a favourite. Moffat even called him "the man who showed us how to write Doctor Who".

He was the youngest ever commissioned officer in the Queen's Own Cameron Highlanders, serving in Burma.

Russell T. Davies has compared his dialogue in The Talons of Weng-Chiang: Part One (1977) with the work of the esteemed screenwriter Dennis Potter.

I am not a fan of Sherlock Holmes but I am a fan of that fictitious Victorian period, with fog, gas lamps, Hansom cabs and music halls. We look back on it and say that's what it was like, although of course it wasn't - people were slaving in dark, satanic mills and starving in London gutters.

[speaking in 1977 about his period as script editor on Doctor Who (1963)] Of course it's no longer a children's programme. Parents would be terribly irresponsible to leave a six-year-old to watch it alone. It's geared to the intelligent fourteen-year-old, and I wouldn't let any child under ten see it. If a little one really enjoys peeping at it from behind the sofa, until Dad says "It's all right now - it's all over," that's fine. A certain amount of fear is healthy under strict parental supervision. Even then I'd advise half an hour to play with Dad and forget it before a child goes to bed. That's why we switched the time-slot from 5.15 to after 6.00, when most young kids are in the bath.

The Deadly Assassin (The Deadly Assassin: Part One (1976)) was, I think, the first Doctor Who in years that did not feature a monster. We decided instead to go for these surrealistic sequences of episode three. This meant putting all our film effort into one episode. And this meant writing the other three episodes totally for studio. David Maloney took all these difficulties in his stride, as he always does, and directed the show brilliantly.

(On Genesis of the Daleks) I said 'Unless somebody can come up with something different, I'm not doing a Dalek story'. A lot of pressure was put on me to change my mind. Then Barry (Letts) came up with the idea of calling it 'Genesis' and having this Davros character who had actually invented the Daleks in his own image. This gave the story some scope and we could have some acting going on. I'd looked at the viewing graphs for the Daleks, and saw that every time they were brought back they were popular in week one, as a lot of people had perhaps never seen them before, and then the graph would go straight down, because they were boring.

(On The Time Warrior) They wanted to do a historical, which they hadn't attempted for some time. Now, I hate Doctor Who (1963) in the history mode, because I think it's too whimsy and twee. So I compromised and offered them a story mixing science fiction with a kind of pseudo-history. The Sontarans came after I'd been reading some heavy tome on war - it was terribly Teutonic and all about the Fatherland and so on. I saw the cloned Sontarans gaining sustenance from their shops wherein they are monitored to make sure they don't spend too much time on the recharding. If they do, I saw a kind of umbilical regression surging down to kill them.

The bifurcated hand was my mistake - it was very difficult for the actor to pull out his laser or whatever. Other stuff in that script was Professior Ruebish, a favourite character of mine, because I like zany professors and that wonderful sexist line about Sarah, where Linx says she is useless because her thorax shows her to be the female of the species! The name Irongron was inspirited from the Danish names of warriors, while Bloodaxe was just hokey 'Robin Hood' style - you know, terribly butch men living in castles.