Born in the Midlands of England, and educated at King Edward VI Aston, Nathan-Turner showed an early interest in acting and theatre. He joined the BBC as a floor assistant in the 1960s, and first worked on Doctor Who in 1969 as part of the floor crew at the time that the series was recorded in Studio D of the Lime Grove Studios. His first story was The Space Pirates in 1969, in which he was credited as John Nathan. He came from a non-practising Jewish family.

He later served as production unit manager under Graham Williams from 1977 to 1979. He accepted the position of producer for Season 18, the last that featured Tom Baker's portrayal of the central character, the Doctor. He subsequently cast the next three actors to play the role: Peter Davison (1981—1984), Colin Baker (1984—1986) and Sylvester McCoy (1987-1989 & 1996).

Nathan-Turner's experience under Graham Williams helped form his views for the future of the series. He strongly felt that many people, both within the programme and in the viewing public, no longer took Who seriously. It was also generally agreed that Tom Baker had been allowed too much influence of the direction of the series and that Williams was not willing to confront him. Nathan-Turner, along with the new Script Editor, Christopher H. Bidmead, decided that Baker needed to be reined in and made to take the role more seriously. For Nathan-Turner's first season in charge of the show, former Doctor Who producer Barry Letts was asked to return in the role of Executive Producer, and acted as an advisor for Nathan-Turner in this period.

Nathan-Turner decided to begin a sweeping overhaul of the series, replacing the original theme music with a more contemporary electronic beat. He also introduced revamped title and credit sequences, featuring a new face shot of Baker (the original having been taken in 1974). He commissioned costume designer June Hudson to make a new outfit for Tom Baker, giving her carte-blanche (even giving permission to remove the trademark scarf if she liked, which she only gave a new burgundy and purple colour pattern instead). He did, however, insist that question marks be added to the costume. Unlike most of the previous producers, Nathan-Turner had no writing experience. As a result, choosing stories was left largely to script editors. Nathan-Turner's first major story influence was bringing back the Master, the logistics of which he left to Bidmead to deal with. After Nathan-Turner's first season in charge, both Bidmead and Letts left the series. Letts was never replaced in Nathan-Turner's time in charge of the show, while Bidmead was briefly replaced by Antony Root, and then more permanently by Eric Saward, who would be script editor for much of Nathan-Turner's time in charge of the show.

By the end of Season 19, Nathan-Turner decided that the series would benefit by re-using earlier villains and characters ... Earthshock enjoyed considerable acclaim with the return of the Cybermen. Season 20 saw the return of the Black Guardian, Omega, and the Brigadier. The re-use of classic villains often proved difficult for both script editor Eric Saward and the writers. Nathan-Turner, however, was largely focused on generating publicity for the series and snagging well-known stars. He also wanted to avoid using directors and writers from the previous periods, the few exceptions being director Pennant Roberts and writers Terrance Dicks and Robert Holmes.

Having served as producer for so long, and having a more public persona than previous incumbents, Nathan-Turner was often the object of intense scrutiny by the series' fans, who often referred to him as "JNT" or "JN-T". Decisions such as how he selected Colin Baker for the role of the Sixth Doctor (he reportedly "made him laugh at a party"), and the casting of Bonnie Langford as his 2nd companion are still a topic of discussion in the Doctor Who fan community twenty years later. His tenure coincided with a period of large growth in the show's fan base in the United States, thanks to repeated showings on affiliates of the American Public Broadcasting Service (PBS). Nathan-Turner was a familiar face among the many Doctor Who celebrities who made spot-appearances during PBS pledge drives in support of more Who in America.

Nathan-Turner made a number of controversial changes to the series. In Season 19, he had the sonic screwdriver destroyed in The Visitation. (Eric Saward, who wrote the story, initially only meant to remove it for a single episode as he thought that the Doctor "had an entire cabinet full of them".) Early in his producership, the show was moved from its Saturday evening slot to air on Monday and Tuesday of each week. Despite a degree of outrage, it did lead to a large increase in viewing figures. He also oversaw the removal of K-9 from the series ... though he did commission the pilot of K-9 and Company. He even allowed the TARDIS to lose its iconic police box shape at one point, though its distinctive interiors ... modernised in high-white ... were more heavily used than at any time since the 1960s, giving the (now multiple) companions an on-screen home.

Nathan-Turner was arguably the highest-profile producer of the original series, and his reign was at times controversial. His changes to the programme were initially well-received by Doctor Who fans, to whom he extended an unprecedented degree of welcome. Editors of non-professional magazines or "fanzines" would be granted interviews by Nathan-Turner in the Who production office. Although he did not divulge the contents of forthcoming storylines in such conversations, he would speak in-depth and at length about his approach to producing the show.

This openness to fandom proved a double-edged sword for Nathan-Turner. As his tenure on the series lengthened, and especially when the show's ratings began to drop, fan criticism of Nathan-Turner became more prevalent. Fanzines began to blame him for decisions made about the series, whether he was responsible for them or not. The series was placed on hiatus at the end of its 1985 season. By the time it returned in September 1986, his professional relationship with Saward was rapidly deteriorating.

Nathan-Turner's lack of first-hand experience in scripting and direction contributed to his tendency to be distrustful of some of the crew around him. Former director-turned-writer Peter Grimwade had agreed to direct Resurrection of the Daleks, but Nathan-Turner removed him from the post ... mainly due to his perception of being snubbed by Grimwade when he did not invite him to a dinner party. He also became upset when the replacement director, Matthew Robinson, discussed a camera shot with Saward ... Nathan-Turner insisting that a script editor had no place in such matters. Grimwade later made a thinly-veiled parody of Nathan-Turner on the series Dramarama called The Come-Uppance of Captain Katt, while Saward made hurtful remarks about him in an unguarded magazine interview just after leaving the series in 1986.

However, Nathan-Turner, who had great organisational flair, knew the BBC's ways intimately and often fixed deals to the show's advantage. Supporters of his reign argue that the producer was not solely to blame for the series' decline in ratings and that the hierarchy at the BBC, funding issues, ratings calculation methods, the decline of in-house drama production, and the decision to schedule the series opposite the popular Coronation Street should all share some responsibility.

Following the difficulties of Season 23, some believe that he in fact was growing tired of the programme. In a documentary about the "end" of the series, some people claimed that Nathan-Turner approached the BBC about leaving the series, but had been told that if he left the series would be cancelled. Some even state that despite the controversy, Nathan-Turner was likely the only thing left holding the suffering series together for its last three seasons.

Criticism of Nathan-Turner's production of Doctor Who ranged from including too many back-references to the casting of guest stars from light entertainment. As mentioned, he was criticised for choosing Bonnie Langford as a companion: though Langford had been a child lead in ITV's 1970s adaptation of Just William, she was better known as a musical theatre performer and dancer. It was also felt that he chose companions because of "gimmicks", such as the character of Tegan Jovanka (an Australian flight-attendant) in the hope of getting "cheap tickets" for possible filming abroad. This was also true for the American character Peri Brown (in an attempt to endear the show more to the US). He was also criticised, at the time, for casting lead actors Colin Baker and Sylvester McCoy, whom some thought were unsuitable for the role.

Some fans feel the quality of the series was improving up until its cancellation in 1989 although ratings sank to all time lows. Nathan-Turner also helped introduce the popular character of Ace at the end of Season 24. By the end of Season 26, Nathan-Turner was aware that the show would likely not return the next year and asked Cartmel to add more weight to the conclusion of the final story, resulting in the Doctor's speech at the end of Survival.

Nathan-Turner continued to be involved in Doctor Who-related events, including the show's 20th Anniversary celebrations at Longleat in 1983 and co-writing the 1993 charity special Dimensions in Time, and co-presenting the BSB 31 Who programmes during their 1990 Doctor Who Weekend, until shortly before his death. He made his final contribution to the series when he appeared in a DVD retrospective on Resurrection of the Daleks in 2001.

Nathan-Turner died of liver failure just over a year before the announcement by the BBC that the show would be revived, with new episodes to air beginning in 2005. He was survived by his long-term partner, Gary Downie, a production manager on Doctor Who. Downie died on 19 January 2006. Downie spoke, in an interview with Doctor Who Magazine, of his time with Nathan-Turner. Nathan-Turner lived for many years in Saltdean, Brighton.