Richard David James was born to Welsh parents Lorna and Derek James in St. Munchins Limerick Regional Maternity Hospital, Ireland. He grew up in Lanner, Cornwall; he enjoyed (along with two older sisters) a "very happy" childhood during which they, according to James, "were pretty much left to do what [they] wanted." He "liked growing up there, being cut off from the city and the rest of the world". James attended Redruth School, located in Redruth, Cornwall.

According to musician Benjamin Middleton, James started producing music at the age of 12. As a teenager he was a disc jockey at Shire Horse in St. Ives, with Tom Middleton at the Bowgie Inn in Crantock, and also along the numerous beaches around Cornwall. James studied for a National Diploma in Engineering from 1988 to 1990 (aged 16 to 18) at Cornwall College. When talking about his studies, James has said that "music and electronics went hand in hand." James graduated from college; according to an engineering lecturer, however, he often had his headphones on during practical lessons, "no doubt thinking through the mixes he'd be working on later".

In 1989 James met and befriended Grant Wilson-Claridge when working as a DJ on alternate weeks at the Bowgie pub, near Newquay in Cornwall. Wilson-Claridge was intrigued by James's sets and was surprised to discover that James was playing tapes of his own music.

James' first release was the 12-inch EP Analogue Bubblebath on Mighty Force Records in 1991. It was first released under the moniker Aphex Twin, later changed to AFX. The track "En Trance to Exit" was made in collaboration with Tom Middleton, also known as Schizophrenia. The EP got on the playlist of Kiss FM, an influential London radio station, which helped the release to become a success.

In 1991 James founded Rephlex Records with Wilson-Claridge to promote "innovation in the dynamics of Acid — a much-loved and -misunderstood genre of house music forgotten by some and indeed new to others, especially in Britain."

Between 1991 and 1993, James released two Analogue Bubblebath EPs as AFX, and an EP under Bradley Strider, Bradley's Beat. James moved to London to take an electronics course at Kingston Polytechnic, but at the time admitted to David Toop that his "electronics studies were already slipping away as a career in the techno business took precedence." After quitting his course, James remained in London and released a number of albums and EPs on Warp Records and other labels under many aliases including AFX, Polygon Window, and Power-Pill. A number of James' tracks (released under the aliases Blue Calx, The Dice Man, and others) appeared on various compilations. Local legend has it that James lived on the roundabout in Elephant and Castle, South London during his early years in the capital - in fact he lived in a nearby disused bank.

The first full-length Aphex Twin album, Selected Ambient Works 85-92, was released in 1992 on R&S Records. It received high ratings and praise from critics. John Bush of Allmusic described it as a "watershed of ambient music". Rolling Stone wrote of the album: "Aphex Twin expanded way beyond the ambient music of Brian Eno by fusing lush soundscapes with oceanic beats and bass lines." Pitchfork's review called it, "among the most interesting music ever created with a keyboard and a computer." Critics also noted that the songs were recorded on cassette and that the sound quality was "relatively poor".

In 1992, he also released the EPs Xylem Tube EP and Digeridoo (first played by DJ Colin Faver on London's Kiss FM) as Aphex Twin, as Power-Pill the Pac-Man EP based on the arcade game Pac-Man, and two of his four Caustic Window EPs. The song "Digeridoo" reached #55 on the UK charts, and was later described as foreshadowing drum and bass by Rolling Stone. "Digeridoo" was recorded initially for the benefit of FIZZ-BOMB (at the Shire Horse, St Ives, Cornwall). These early releases came out on Rephlex Records, Mighty Force of Exeter, and R&S Records of Belgium.

In 1993, James released Analogue Bubblebath 3. He also released a single titled "On"; his second Bradley Strider EP, Bradley's Robot; two more Caustic Window EPs; and his first releases on Warp Records, Surfing on Sine Waves and "Quoth" under the alias Polygon Window.

Warp Records pressed and released a follow-up to Selected Ambient Works 85-92, Selected Ambient Works Volume II in 1994. The sound was much less beat and melody-driven than the previous volume. All of the track names were described with pie chart symbols, each of which was meant to be paired with a corresponding image in the album jacket, with exception for one song, which was definitely named "Blue Calx". To decipher song titles, listeners had to pair each numbered symbol with the correct image (for example, the first title, which is often labeled cliffs, is realized by pairing the first symbol with the first image, which is that of a rocky cliffside). James claimed in The Wire magazine and other media that these songs were inspired by lucid dreams and synesthesia. Other releases are a fourth Analogue Bubblebath; GAK, derived from early demos sent to Warp Records; and Classics, a compilation album that includes "Digeridoo" and the Xylem Tube EP.

For his 1995 release, ...I Care Because You Do, James used an image of his face for the album cover, a motif that would continue on many of his later records. The album was a compilation of songs composed between 1990 and 1994 and represented a mish-mash of Aphex Twin's various music styles. This was James's last record of the 1990s to use mostly analogue synthesizers. He commissioned Western classical-music composer Philip Glass to create an orchestral version of one of the songs from this album, “Icct Hedral,” which appeared on the Donkey Rhubarb EP.

In 1995 (primarily with Hangable Auto Bulb, a near anagram of Analogue Bubblebath), James began releasing more material composed on computers, combining a jungle sound with nostalgic childhood themes and computer-generated acid lines.

James's early adoption of software synthesizers predated the later popularity of using computers to make music. In late 1990s, his music became more popular and mainstream, as he released Richard D. James Album (which included the previously released Girl/Boy EP in its US release) and Expert Knob Twiddlers (a collaboration with fellow dance producer µ-ziq) in 1996, "Come to Daddy" in 1997 (#36 on UK charts) and "Windowlicker" in 1999 (#16 on UK charts). Two pop songs that heavily use Digital Signal Processing (DSP) techniques, "Come to Daddy" and "Windowlicker" were shown on MTV and became cover features for music magazines such as NME. The videos for both singles were directed by British artist Chris Cunningham and caused controversy on release because of their disturbing images and themes.

In 1998 Aphex Twin's track "[rhubarb]" (from Selected Ambient Works Volume II) appeared as part of the BBC's digital widescreen test transmission, which was on loop for many months as the service was introduced across the UK.

In 2001 Aphex Twin released drukqs, a two-CD album that featured prepared piano songs influenced by Erik Satie and John Cage. Many of the tracks' names are written in the Cornish language (e.g., 'jynweythek' translatable as 'machinemusic'). Also included were abrasive, fast, and meticulously programmed computer-made songs. Rolling Stone described the piano songs as "aimlessly pretty". Some reviewers concluded that drukqs was released as a contract breaker with Warp Records—a credible guess, as James's next big release was released on his own Rephlex label. James claimed to interviewers he had accidentally left an MP3 player labelled "Aphex Twin—unreleased tracks" on a plane, containing a large set of new songs, and rushed the album release to preempt an Internet leak. He also released a short EP titled 2 Remixes By AFX the same year as Drukqs. It featured two remixes, the originals being from 808 State and DJ Pierre. In addition, there is one untitled third track that consists mostly of high-pitched sounds.

In late 2004, rumours of James's return to an acid techno-based sound were realised with the Analord series, an 11-part series of LPs with 42 total tracks, averaging 2–4 tracks per LP. The series was created by playing and sequencing analogue and digital electronic music equipment such as synthesizers and drum machines. The series was recorded on magnetic tape and then later pressed on vinyl.

James was meticulous about the whole process of recording, mastering, and pressing. James has said Rephlex Records was strict on quality control, trying out various pressing-plant companies until they felt it sounded perfect. To James's ears, vinyl or tape is better than digital, as no two copies are the same. However, label co-owner Grant Wilson-Claridge convinced James to release a digital CD, Chosen Lords, which included 10 selected songs from the Analord series, with some tracks slightly altered to improve the flow of the album. For the Analord records, James used his collection of Roland drum machines, bought when they were still at bargain prices. Some of the record labels display pictures of rare synthesizers like the Synton Fenix, and the notoriously difficult to program Roland MC-4 sequencer (a sequencer with a reputation for excellent timing), as well as the legendary Roland TB-303.

Media reports indicate Aphex Twin is now recording under The Tuss. Rephlex Records has denied that Aphex Twin is the Tuss, but Aphex Twin fans and the media have ignored Rephlex's denial and the Tuss is treated as yet another Aphex Twin project.

In March 2009 Steve Beckett of Warp Records announced a new album for a possible 2009 release.