He began his career in television as a six-months trainee at Granada Television in Manchester, where he worked as a researcher. One of his first projects at Granada would become his best known: the Up Series, which began in 1964 as a profile of fourteen seven-year-old children for the current affairs series World In Action. As a researcher and assistant to Canadian Director Paul Almond, Apted was involved in selecting the children. Though it began as a one-shot documentary, the series has become an institution, revisiting the subjects every seven years, with Apted directing the later episodes in the series. It follows Apted's thesis that the British class system remains largely in place, and is premised on the Jesuit motto "Give me a child until he is seven and I will give you the man." The series looks at the lives of this sample of British people over the years; the latest instalment, 56 Up, was produced in 2012. It won a Peabody Award in 2012 "for its creator’s patience and its subjects’ humanity."

Apted made his first feature film in 1972, The Triple Echo, starring Oliver Reed and Glenda Jackson, and he directed two films for David Puttnam. The Triple Echo was entered into the 8th Moscow International Film Festival. He alternated this work with working on the TV series Play for Today. He directed six plays including Stronger than the Sun, written by Stephen Poliakoff and starring Francesca Annis as a young woman who places her life in danger to expose a crime, a theme Apted has returned to several times.

In 1979 he directed the Hollywood-financed Agatha, featuring Vanessa Redgrave. The majority of Apted's feature films since then have been based around a female protagonist. He went to the United States in 1980, where he directed Coal Miner's Daughter, which received seven Academy Award nominations, winning best Actress for Sissy Spacek. Both Spacek and Loretta Lynn, the subject of the film, have said that they believe Apted's outsider point of view was crucial to the movie's success in securing the participation of Appalachian residents and to the avoidance of stereotypes that previously had marred portrayals of mountain culture. Sigourney Weaver and Jodie Foster have also earned Academy Award nominations for their work in Apted-directed films.

During his seven-year stay at Granada, Apted also directed a number of episodes of Coronation Street, then written by Jack Rosenthal. Apted and Rosenthal went on to collaborate on a number of popular television and film projects including the pilot episodes for The Dustbinmen and The Lovers. They worked together again in 1982 for the TV movie P'tang, Yang, Kipperbang, the first film commissioned by Britain's Channel 4. In 1976 he directed a play in the Granada TV Series Laurence Olivier Presents. The episode was The Collection by Harold Pinter. The play starred Laurence Olivier, Malcolm McDowell, Alan Bates and Helen Mirren.

Apted has also made several films with a strong social message or that deal with an ethical dilemma. In 1983 he directed Gorky Park, a political thriller based on the novel by Martin Cruz Smith, that deals with police corruption in the former Soviet Union. Class Action deals with a corporate whistleblower, and Extreme Measures is about medical ethics. Class Action was entered into the 17th Moscow International Film Festival. In 1999, Apted directed the James Bond film The World Is Not Enough.

In addition to feature films, Apted has continued directing documentaries, including Bring on the Night, a feature-length concert film about the making of Sting's first solo album. In 1988/9 he directed the documentary The Long Way Home, which chronicled the UK, US and USSR adventures of Boris Grebenshikov, the first Soviet underground musician allowed to record in the West. Before the making of Thunderheart, Apted made the documentary Incident at Oglala about convicted murderer Leonard Peltier. Incident at Oglala then informed Thunderheart in the casting of actors for the fiction film. In 1997, he explored the creative process in Inspirations through candid discussion with seven artists from diverse media, including music, painting, dance, sculpture, and architecture.

In a departure from his earlier work, from 1992 to 1994, Apted ventured into China's rapidly changing popular culture. In a project backed by Trudie Styler, Apted directed Moving the Mountain, a feature documentary which probed the origins of the 1989 protests in Tiananmen Square and the consequences of the movement in the lives of several of the movement's student Leaders.

On 29 June 2003 he was elected President of the Directors Guild of America. He returned to television, directing the first three episodes of the TV series Rome (2005). Apted directed Amazing Grace which premiered at the closing of the Toronto International Film Festival in 2006. He was appointed a Companion of the Order of St Michael and St George (CMG) in the 2008 Birthday Honours.

In 2006, Apted directed The Official Film of the 2006 FIFA World Cup, narrated by Pierce Brosnan.

Apted was the collaborator and subject of the documentary: Michael Apted – Visions on Film, by Artist and filmmaker Melinda Camber Porter.

Michael Apted married Paige Simpson, his third wife, in January 2014. Apted is divorced from his second wife, the Screenwriter Dana Stevens, with whom he has a 12-year-old son, John. From his first marriage to Jo Apted he had two sons, Paul and Jim. Paul Apted was a sound Editor who worked on movies such as The Wolverine, and died on 4 July 2014 from colon cancer. In 2007 Apted became a father for the fourth time to a girl, Lily Mellis, who lives with her mother Tania Mellis in California.