Anti-Flag was originally formed in Pittsburgh, Pennsylvania in 1988. The band name originates from the experiences that the founders had in their hometownWhen the two would go to local shows, they often saw patrons of the shows chanting slogans for "freedom not fascism" while waving the American Flag and sporting the flags with "x"s over them on their jackets. However, these same patrons would constantly participate in violence against those who did not completely agree with their point of view. Justin and Pat saw the brandishing of the American Flag and using it as a tool against others as a form of fascism.

During this time, various guitarists and bassists moved in and out of the band, including Justin's sister, Lucy Fester. The band failed to solidify, and it fell apart after playing just one show.In 1993, Justin and Pat formed a new band, now with Andy Flag on bass, which they again named Anti-Flag. In 1996, the band released their first album, Die for the Government, on New Red Archives. Andy Flag left the band in the Summer of 1996 because of personal disputes between himself and Justin. For a brief time after Andy's departure in 1996, Sean Whelan of Pittsburgh band the Bad Genes filled in on bass. It was during this time that Sean was also playing in another band (57 Defective) with guitarist Chris Head, who he introduced to the band.

In early 1997 Pittsburgh guitarist Chris Head began filling in on bass. In late 1997, Jamie Cock took over as the new bassist, moving Chris Head over to second guitar, which he preferred. The current lineup finalized in 1999 when Chris Barker, also known as Chris #2, replaced Jamie Cock on bass.

In 1999, Anti-Flag released the album A New Kind of Army on Go-Kart Records/A-F Records (A-F Records being Anti-Flag's own independent label). The album addressed a wide variety of topics such as political corruption, racism, fascism, troubled youth, police brutality, and unity within the American youth. The cover art page unfolded into a poster featuring the phrase "Too smart to fight. Too smart to Die. Join now. A new kind of army."

In 2000, Anti-Flag was invited to participate in Vans Warped Tour. During this time, the members of Anti-Flag met the likes of NOFX's Fat Mike, owner of the Fat Wreck Chords record label. This meeting spawned a friendship that would lead to Anti-Flag's release of two albums on the label.

In 2001, Anti-Flag teamed with legendary punk producer Mass Giorgini to record the album Underground Network,released on Fat Wreck Chords. The release of the album is arguably the band's breakout from the hardcore underground to a more mainstream spotlight. The album continued to address the issues of fascism (specifically neo-Nazis infiltrating the "hardcore scene") and the United States' foreign policy. The album was the first to contain the now commonplace booklet filled with essays from historians and political commentators, most notably Professor Howard Zinn. In February 2002, Anti-Flag released the album Mobilize on A-F Records. The album featured new songs as well as eight live tracks of songs from other albums. In the wake of the September 11th terrorist attacks on the United States, Anti-Flag spoke out against the push for war by the United States government. During this time, many music stores pulled Anti-Flag's records from shelves, as their music was labelled as "anti-American."In 2003, Anti-Flag released the album The Terror State on Fat Wreck Chords. The album primarily focused on criticizing the Bush Administration's handling of the War on Terrorism. Again, the album contained a booklet full of essays from the band as well as other political commentators. The album contains a song whose lyrics were originally written by Woody Guthrie entitled "Post-War Breakout." The track's music was arranged by the members of Anti-Flag, as Guthrie had never committed the arrangements to paper.

In 2005, Anti-Flag signed a two-album record contract with major label RCA. The first of these two albums, For Blood and Empire, was released on March 21, 2006. The album's main focus is the band's criticism of the mishandling of the War on Terrorism by the United States Government. The song 'This Is The End (For You My Friend)' from the album For Blood and Empire is featured in the video game, Madden NFL 2007 and on NHL 07. They finished their huge "War Sucks, Let's Party" United States headlining tour in April and work on some side projects like African Well Fund and Start to Finish MS now.

Throughout Anti-Flag's career, many other bands have been added to the roster of the band's own label, A-F Records. These bands include The Code, Much the Same, The Vacancy, The Unseen, Modey Lemon and more.

On November 25, Anti-Flag revealed on their homepage that their newest album was titled The Bright Lights of America, Produced by Tony Visconti of David Bowie and Morrissey fame. It was released on April 1, 2008. The single "The Bright Lights Of America" was released exclusively on iTunes on February 12, 2008. A video of the song was released a couple of weeks later.