You have the possibility to give light a dimension in time,

—Jonas Mekas, 1978

In 1944 Mekas left Lithuania because of war. En route, his train was stopped in Germany and he and his brother, Adolfas Mekas, were imprisoned in a labor camp in Elmshorn, a suburb of Hamburg, for eight months. The brothers escaped and were detained near the Danish border where they hid on a farm for two months until the end of the war.

After the war, Mekas lived in displaced person camps in Wiesbaden and Kassel. From 1946-48, he studied philosophy at the University of Mainz and at the end of 1949, he emigrated with his brother to the U.S., settling in Williamsburg, Brooklyn, New York. Two weeks after his arrival, he borrowed the money to buy his first Bolex 16-mm camera and began to record moments of his life. He discovered avant-garde film at venues such as Amos Vogel’s pioneering Cinema 16, and he began screening his own films in 1953 at Gallery East on Avenue A and Houston Street, and a Film Forum series at Carl Fisher Auditorium on 57th Street.

In 1954, he became editor of Film Culture, and in 1958, began writing his “Movie Journal” column for The Village Voice. In 1962, he co-founded Film-Makers' Cooperative (FMC) and the Filmmaker’s Cinematheque in 1964, which eventually grew into Anthology Film Archives, one of the world’s largest and most important repositories of avant-garde films. The films and the voluminous collection of photographs and paper documents (mostly from or about avant garde film makers of the 1950-1980 period) were moved from time to time based on Mekas' ability to raise grant money to pay to house the massive collection. At times, Mekas personally paid its housing rent and, at low points in external funding, he had to restrict access to the collection. Easily, he can be credited with single-handedly saving large portions of the avant garde films and associated materials.

He was part of the New American Cinema, with, in particular, fellow film-maker Lionel Rogosin. He was heavily involved with artists such as Andy Warhol, Nico, Allen Ginsberg, Yoko Ono, John Lennon, Salvador Dalí, and fellow Lithuanian George Maciunas.

In 1964, Mekas was arrested on obscenity charges for showing Flaming Creatures (1963) and Jean Genet’s Un Chant d’Amour (1950). He launched a campaign against the censorship board, and for the next few years continued to exhibit films at the Film-makers’ Cinemathèque, the Jewish Museum, and the Gallery of Modern Art.

From 1964-1967, he organized the New American Cinema Expositions, which toured Europe and South America and in 1966 joined 80 Wooster Fluxhouse Coop.

In 1970, Anthology Film Archives opened on 425 Lafayette Street as a film museum, screening space, and a library, with Mekas as its director. Mekas, along with Stan Brakhage, Ken Kelman, Peter Kubelka, James Broughton, and P. Adams Sitney, begin the ambitious Essential Cinema project at Anthology Film Archives to establish a canon of important cinematic works.

Mekas' own output ranging from narrative films (Guns of the Trees, 1961) to documentaries (The Brig, 1963) and to “diaries” such as Walden (1969); Lost, Lost, Lost (1975); Reminiscences of a Voyage to Lithuania (1972) and Zefiro torna (1992) have been screened extensively at festivals and museums around the world. In 2001, he released a five-hour long diary film entitled As I Was Moving Ahead, Occasionally I Saw Brief Glimpses of Beauty, assembled by hand from an archive of fifty years worth of recordings of his life. Peter Sempel filmed Jonas Mekas in the film Jonas in the Desert (1994). Mekas made an 85-minute film showing clips of 160 filmmakers he knew in Birth of a Nation (1995).

Mekas expanded the scope of his practice with his later works of multi-monitor installations. Presented as total immersive environments, they offer a new experience of his classic films and have been exhibited at the 51st Venice Biennial, PS1 Contemporary Art Center, and the Jonas Mekas Visual Arts Center.

In 2004, the dormant Eero Saarinen-designed TWA Flight Center at JFK Airport briefly hosted an art exhibition called Terminal 5 curated by Rachel K. Ward and featuring the work of 18 artists including Mekas. The show featured work, lectures and temporary installations drawing inspiration from the idea of travel — and the terminal's architecture. The show was to run from October 1, 2004 to January 31, 2005 — though it closed abruptly after the building itself was vandalized during the opening party.

Beginning in the fall of 2006, Mekas planned to film 365 short videos for Apple Computer's Video iPod, releasing one a day on his website.

Since the 1970s, he has taught film courses at the New School for Social Research, MIT, Cooper Union, and New York University.

Mekas is also a well-known Lithuanian language poet and has published many of his poems and prose in both Lithuanian and English. He has published many of his journals and diaries including "I Had Nowhere to Go: Diaries, 1944-1954," "Letters from Nowhere," and "Just like a Shadow," as well as his articles on film criticism, theory, and technique.

On November 10, 2007, Jonas Mekas opened Jonas Mekas Visual Arts Center in Vilnius.

In its August 2010 the magazine Dazed & Confused published a 8 pages spread about Jonas Mekas.