Trudell was born in Omaha, Nebraska on February 15, 1946, as the son of a Santee Dakota father and a Mexican mother. He grew up in small towns near the Santee Sioux Reservation in northern Nebraska near the southeast corner of South Dakota. He was educated in local schools and also in Santee Dakota culture.

In 1963 when 17 years old, Trudell dropped out of high school and left the Midwest by joining the US Navy. He served during the early years of the Vietnam War and stayed in the Navy until 1967.

In 1968, Trudell married his first wife, Fenicia "Lou" Ordonez.

After leaving the military, Trudell had become involved in Indian activism. In 1969, he became the spokesperson for the United Indians of All Tribes' occupation of Alcatraz Island. This was a mostly student-member group that had developed in San Francisco. Trudell went to Alcatraz a week after the occupation started. He used his background in broadcasting and ran a radio station from the island through a cooperative arrangement with students at the University of California, Berkeley, broadcasting at night over the Berkeley FM station. The show was called Radio Free Alcatraz. He discussed the cause of the occupation and American Indian issues, and played traditional Native American music. He criticized how "the system today is only geared toward white needs." He spoke for the many Indians who believed they did not fit in with the then majority European-American population of the nation. He became a spokesperson for the occupation specifically and for the Alcatraz-Red Power Movement generally, as the author Vine Deloria, Jr. named it. Trudell was the spokesman for the nearly two-year-long occupation, until 1971.

In 1972, Trudell married Tina Manning, an Activist of the Duckwater Shoshone Tribe. They had three children together: Ricarda Star, Sunshine Karma, and Eli Changing Sun. In February 1979, Tina (who was pregnant), the children and her mother Leah Hicks-Manning were all killed in a fire at her parents' house on the Duck Valley Reservation. Her father Arthur survived. Trudell was out of town.

In 1975 Trudell was arrested on charges of assault, felonious assault and assault with a deadly weapon. He had gone to a reservation trading post to try to get better food for senior residents. He tried to pay using food stamps, but the trading post did not accept them. The police report said that he fired a shot inside the store.

In 1979, John Trudell met musical Artist and Activist Jackson Browne and became more interested in the musical world (and recording albums and performing his own compositions in live venues).

Trudell recorded an album A.K.A Grafitti Man ("graffiti" was misspelled in the title) with Kiowa Guitarist Jesse Ed Davis that was originally available on cassette tape format only. This comports with the practice Common to American indigenous and other so-called minorities of distributing music mixtapes captured live at group events and copied and distributed through non-commercial channels, like those of the San Francisco-based rock group Grateful Dead, Native American powwow music performances in general, and African American gatherings whence came the expression Each One Teach One, Common also to an emerging grassroots movement that was arguably itself a response to the reactionary madness of slavery and/or military-industrial/imperialist hegemony flourishing in the 1980s.

Trudell often used his poetry as lyrics for recordings, and began in 1982 to set them to traditional American Indian music, which also in the 1980s eventually led to the recording of A.K.A Graffiti Man, as he struggled to make sense of bewildering situations that confronted him, including the loss of so many loved ones.

Other musical releases (many with his band Bad Dog) include A.K.A Grafitti Man (1986), Heart Jump Bouquet (1987), Blue Indians (1999), Descendant Now Ancestor (2001), Bone Days (2001), Live A Fip (2003), Madness and The Moremes (2007), Crazier Than Hell (2010), Wazi's Dream (2015).

In late 1988, Australian rock band Midnight Oil invited Trudell (as Graffiti Man) to tour with them during their From Diesel and Dust to the Big Mountain world tour. They billed Trudell's part of the show as "Native American Activist performance." Members of Midnight Oil played traditional instruments, sang in native American languages, and accompanied songs with heavy psychedelic Hendrix-style guitar, accompanying Trudell. This exposure brought Trudell new and larger audiences.

Trudell created a career as an actor, performing in roles in "Pow Wow Highway" (1989), Thunderheart (1992), On Deadly Ground (1995) and Smoke Signals (1998) (as the Radio speaker Randy Peone on K-REZ radio). He was an adviser to the production of Incident at Oglala, directed by Michael Apted and produced by Robert Redford. A kind of companion piece to the fictional Thunderheart, the 1992 documentary explores facts related to the 1975 shooting of two FBI agents at the Pine Ridge Indian Reservation, for which Leonard Peltier was convicted in 1977. In Thunderheart, Trudell played a character who resembles Peltier.

In 1990 John Trudell took part in Tony Hymas's Oyaté project.

In 1992 Trudell remade and re-released A.K.A Grafitti Man as an audio CD to substantial critical and popular acclaim.

Trudell also toured in 1993 with Peter Gabriel's global WOMAD (World Music and Dance) production. He was billed as John Trudell, performing his traditional songs and reading his poetry.

Arguably his greatest musical success came with the 1994 album Johnny Damas & Me that was described as "a culmination of years of poetic work, and an Example of a process of fusing traditional sounds, values, and sensibilities with thought-provoking lyrics, this time with urgent rock and roll."

Dreamkeeper (2003) "The Legends of American Nations Come to Life" features several traditional native stories. Trudell played a character named Coyote in a story about A Spider and Coyote.

In 2004, Trudell testified in the federal trial of Arlo Looking Cloud, an Oglala Lakota American Indian Movement (AIM) member charged in the kidnapping and murder of Anna Mae Aquash, the highest-ranking woman in AIM, in December 1975. Trudell testified that Looking Cloud had told him that John Graham, another low-level AIM member, was the gunman in the murder. Trudell identified Graham from photographs. Looking Cloud was convicted in 2004 and sentenced to life imprisonment.

The filmmaker Heather Rae spent more than a decade making a documentary about Trudell, which was released in 2005. Her intent in Trudell (2005) was to demonstrate how his political and cultural activities were tied to contemporary history and inspired people. The film premiered at the 2005 Sundance Film Festival in the U.S. documentary competition. The movie has received a mixed response among film critics and viewers. Some claimed it to be thought-provoking and touching, while others suggested Rae made a one-dimensional biopic. The song used at the end of the film is "Johnny Lobo" about Trudell by Kris Kristofferson, from his 1995 album A Moment of Forever.

Trudell was in a relationship with Marcheline Bertrand, the mother of Actress Angelina Jolie, at the time of her death from cancer in 2007.

In 2008, Trudell published a book, Lines From a Mined Mind: The Words of John Trudell, a collection of 25 years of poetry, lyrics and essays.

In the 2010s he often shared recent poetic musings and written works-in-progress via social media, such as his Facebook page.

John Trudell was the co-founder of Hempstead Project Heart with Willie Nelson, which became a project of Earth Island Institute in 2012. Hempstead Project Heart is dedicated to raising awareness about the environmental, social, and economic benefits of legalizing industrial hemp in America.

The closing sequence of Alanis Obomsawin's 2014 documentary film Trick or Treaty? is set to Trudell's song "Crazy Horse."

In early December 2015, it was announced that Trudell was in the last stages of terminal cancer. His death was prematurely announced on the evening of December 4, 2015; his publicist asked for a retraction and the stories were largely removed from the websites where they had been posted. Trudell died on December 8, 2015. Before dying, he said: "My ride showed up. Celebrate Love. Celebrate Life."