Fall Out Boy was formed in 2001 in the Chicago suburb of Wilmette, Illinois by friends Pete Wentz and Joe Trohman. Wentz was a "visible fixture" of the relatively small Chicago hardcore punk scene of the late 1990s, performing in various groups such as Birthright, Extinction and First Born, as well the metalcore band Arma Angelus and the more political Racetraitor, "a band that managed to land the covers of Maximumrocknroll and Heartattack fanzines before releasing a single note of music". Wentz was growing dissatisfied with the changing mores of the community, which he viewed as a transition from political activism to an emphasis on moshing and breakdowns. With enthusiasm in Arma Angelus waning, he created a pop punk side project with Trohman as an "easy and escapist" project. Trohman met Patrick Stump, then a Drummer for grindcore band Xgrinding processX and a host of other bands that "never really managed", at a Borders bookstore in Wilmette. While discussing Neurosis with a friend, Stump interrupted the conversation to correct their classification of the band in a conversation that soon shifted to the new band. Stump, viewing it as an opportunity to try out with "local hardcore celebrity" Wentz, directed Trohman to his MP3.com page, which contained sung-through acoustic recordings. Stump intended to try out as a Drummer, but Trohman urged him to bring out his acoustic guitar; he impressed the duo with songs from Saves the Day's Through Being Cool. While Wentz wanted Racetraitor bandmate Andy Hurley in the group as Drummer, Hurley appeared uninterested and too busy.

In a list of the 50 greatest pop-punk albums of all time, Rolling Stone placed Fall Out Boy's 2003 album Take This To Your Grave as the fifth greatest, citing it as "[ushering] in a whole new, genre-blurring scene, in which heavy riffs and a screamo aesthetic mingled with old-fashioned teen heartbreak". In a similar list, Kerrang! magazine placed Take This To Your Grave at number 11 out of 51, describing it as a "blueprint for both break-up records and timeless pop-punk".

Fall Out Boy have been instrumental in the careers of other artists, such as Panic! at the Disco, whom Pete Wentz signed to his record label, Decaydance Records, in late 2004. Several artists, such as You Me at Six and Taylor Swift, have created or performed covers of Fall Out Boy songs as a homage to the band.

While widely considered to be a pop punk band, Fall Out Boy has also been described as pop rock alternative rock, emo, and emo pop, and cites emo group The Get Up Kids as an influence among many other bands. When interviewed for a retrospective article in Alternative Press at the time The Get Up Kids disbanded in 2005, Pete Wentz stated that "Fall Out Boy would not be a band if it were not for The Get Up Kids." Early in the band's career, when Jared Logan was producing the group's debut album, he asked Bassist Pete Wentz what sound the band desired for recording. Wentz responded by "handing over the first two New Found Glory records". Wentz also cites Green Day, Misfits, the Ramones, Screeching Weasel, Metallica, Earth Crisis, Gorilla Biscuits and Lifetime as influences. The band acknowledges its hardcore punk roots as an influence; all four members were involved in the Chicago hardcore scene before joining Fall Out Boy. Wentz described the band's affiliation with the genre by saying "I think the interesting thing is that we are all hardcore kids that are writing pop music...It gives us a different style because at our core we are always hardcore. That aspect is always going to be evident in the music. We are hardcore kids that couldn't quite cut it as hardcore kids." He referred to Fall Out Boy's genre as "softcore": hardcore punk mixed with pop sensibility. Lead singer Patrick Stump, however, is also influenced by artists he listened to while growing up including Prince, Michael Jackson, and David Bowie.

In the wake of the band's multiplatinum success, the "especially extroverted" Wentz became the most publicly visible member of the band. He confided to the press his suicide attempt and nude photos of the Bassist appeared on the Internet in 2006. He gained additional exposure through his clothing line, his Decaydance record label (an imprint of Fueled by Ramen), and eventually a Celebrity relationship with pop singer Ashlee Simpson, which made the two tabloid fixtures in the United States. Due to its increased success from the group's MTV Video Music Award, the group headlined the Black Clouds and Underdogs Tour, a pop punk event that featured The All-American Rejects, Well-Known Secret, Hawthorne Heights, and From First to Last. The tour also featured The Hush Sound for half of the tour and October Fall for half. The band played to 53 dates in the U.S., Canada, and the UK.

Fall Out Boy then headlined the 2007 Honda Civic Tour to promote the album. Though the tour was initially postponed due to personal issues, it would take place with +44, Cobra Starship, The Academy Is... and Paul Wall as supporting acts. The band also headlined the Young Wild Things Tour, an international arena tour featuring Gym Class Heroes, Plain White T's and Cute Is What We Aim For. Inspired by Maurice Sendak's 1963 children's book Where the Wild Things Are, the concert tour and included sets designed by Artist Rob Dobi containing images from the book. The band's "hugely successful" amphitheater tour to promote Infinity led to the release of the 2008 live album Live in Phoenix, consisting of live material recorded during a June 22, 2007, concert at Phoenix's Cricket Wireless Pavilion, a date of the Honda Civic Tour. The disc also a studio cover of Michael Jackson's "Beat It", with Guitarist John Mayer guesting for a guitar solo. The track was released as a single and became a mainstay on the iTunes top ten.

As the release of the new album approached, the band and its management found that they would have to navigate changes in the music industry, facing declining record sales, the lack of a proper outlet for exhibition of music videos, and the burgeoning US economic crisis. To promote the album, Wentz launched a viral campaign in August 2008, inspired by George Orwell's novel Nineteen Eighty-Four (1949), and the autocratic, overbearing Big Brother organization. Folie à Deux, released in December 2008, did not perform as well commercially as its predecessor, Infinity on High. It debuted at number eight on the US Billboard 200 chart with first week sales of 150,000 copies during a highly competitive week with other big debuts, becoming Fall Out Boy's third consecutive top ten album. This is in contrast to the band's more successful previous effort which shifted 260,000 copies in its opening week to debut at number one the chart. Folie spent two weeks within the top 20 out of its 22 chart weeks. It also entered Billboard's Rock Albums and Alternative Albums charts at number three. Within two months of its release, Folie à Deux was certified Gold in the United States by the Recording Industry Association of America (RIAA), denoting shipments of 500,000 copies. The lead single, "I Don't Care", reached a peak at number twenty-one on the Billboard Hot 100, and was certified Platinum by the RIAA for shipments of one million copies.

Rumors and misquotes led to confusion as to what such a break truly meant; Wentz preferred to not refer to the break as a "hiatus", instead explaining that the band was just "decompressing". Fall Out Boy played its last show at Madison Square Garden on October 4, 2009. Near the end, Blink-182's Mark Hoppus shaved Wentz's head in a move Andy Greene in Rolling Stone would later describe as a "symbolic cleansing of the past, but also the beginning of a very dark chapter for the band".

Wentz formed electronic duo Black Cards with vocalist Bebe Rexha in July 2010. The project released one single before album delays led to Rexha's departure in 2011. Black Cards added Spencer Peterson to complete the Use Your Disillusion EP in 2012. Wentz also completed writing a novel, Gray, that he had been working on for six years outside the band, and began hosting the reality tattoo competition show Best Ink. Hurley ventured farther into rock during the hiatus, drumming with multiple bands over the three-year period. He continued to manage his record label, Fuck City, and drummed for bands Burning Empires and Enabler. He also formed heavy metal outfit The Damned Things with Trohman, Scott Ian and Rob Caggiano of Anthrax, and Keith Buckley of Every Time I Die. Despite this, the members all remained cordial to one another; Wentz was Stump's best man at his wedding. The hiatus was, all things considered, beneficial for the group and its members, according to Hurley. "The hiatus helped them all kind of figure themselves out", he explained in 2013. "Especially Joe and Patrick, who were so young. And Pete is a million times better."

Stump and Wentz met up for the first time in several years in early 2012 for a writing session. Wentz reached out to Stump after he penned his letter, as he too felt he was in a dark place and needed a creative outlet. He was at first reluctant to approach Stump, likening the phone call to reconnecting with a lover after years of acrimony. "I know what you need – you need your band", Wentz told Stump. "I think it's kind of weird that we haven't really seen each other this year. We paid for each other's houses and you don't know my kid", Wentz remarked. The result, "three or four" new songs, were shelved with near immediacy, with the two concluding that "it just wasn't right and didn't feel right." Several months later, the two reconvened and wrote tracks that they felt truly represented the band in a modern form. The band decided that if a comeback was in order, it must represent the band in its current form: "We didn't want to come back just to bask in the glory days and, like, and collect a few checks and pretend ... and do our best 2003 impersonation", said Stump. Afterwards, the quartet held an all-day secret meeting at their manager's home in New York City where they discussed ideas and the mechanics of getting together to record. Trohman was the last to be contacted, through a three-hour phone call from Stump. As Trohman was arguably the most excited to begin other projects, he had a list of stipulations for rejoining the band. "If I'm not coming back to this band writing music […] then I don't want to", he remarked. Stump supported Trohman's ambition saying Trohman "needed to be writing more".

The band members' main goal was to reinvent the group's sound from scratch, creating what Trohman called a "reimagining of the band", which focuses more on pop. Sessions were not without difficulties, as the band struggled initially to produce new material. Walker had doubts about the band's volatility, feeling the record would not get made following "meltdown after meltdown". The entire album was recorded in secrecy from the music industry, critics, and fans of the band. While specifically denying that the group's announcement was a reunion because "[the group had] never broke[n] up", the band announced a reunion tour and details of Save Rock and Roll on February 4, 2013. The quartet's announcement included a photo of the group that had been taken earlier that morning of the band members huddled around a bonfire tossing copies of their back catalog into flames at the original location of Comiskey Park, the location of 1979's Disco Demolition Night, a baseball promotional event which involved destroying disco records. A message on the group's website read "when we were kids the only thing that got us through most days was music. It's why we started Fall Out Boy in the first place. This isn't a reunion because we never broke up. We needed to plug back in and make some music that matters to us. The Future of Fall Out Boy starts now. Save rock and roll..." Save Rock and Roll debuted at number one on the Billboard 200 chart, with first week sales of 154,000 copies in the United States, according to Nielsen SoundScan. The arrival of Save Rock and Roll posted the quartet's third-biggest sales week, and earned the group's second career number one on the chart. The band's chart success was best described as unexpected by music journalists. Andy Greene in Rolling Stone called the band's comeback a "rather stunning renaissance", and Entertainment Weekly called the number one a "major accomplishment for a band whom many in the industry had dismissed as kings of a genre whose time had passed".

On November 24, 2014, the title of Fall Out Boy's sixth studio album was announced as American Beauty/American Psycho; the album was released on January 20, 2015. The album's title track premiered on BBC Radio 1 in the UK along with the album's title reveal. American Beauty/American Psycho debuted at No. 1 on the US Billboard 200 with 192,000 first week sales and 218,000 equivalent album units, becoming Fall Out Boy's third No. 1 album. The band played two small venue release shows in January 2015, in London and Chicago. American Beauty/American Psycho was certified platinum in the US on March 1, 2016, after selling 1 millions units. From February through March, the band played at the Australian Soundwave festival for the first time, with two additional side shows in Sydney and Brisbane.

The Fall Out Boy band members were the first inductees to the "Hall of Wood" at the 2015 MtvU Woodie Awards and performed a medley of five songs at the ceremony. This honor is given to artists who have used MTV Woodie Awards as a "launching pad" in achieving chart topping success within their musical careers, thus influencing up and coming bands. The award also recognizes bands "sticking to their roots" and "maintaining their loyal fan base". The group had won the Woodie Award for Streaming for "Grand Theft Autumn" at the first ceremony in 2004.

In 2017, Fall Out Boy were announced as the first winners of Rock Sound's Hall of Fame Award as part of the Rock Sound Awards. In an interview accompanying the band's win, Patrick Stump stated one reason for the band's success is Sugar, We're Goin Down, explaining that the "song changed my life, I have a music career in a large part due to that song". In 2009, Phoenix New Times Writer Martin Cizmar had described Sugar, We're Goin Down as possibly "the most listened-to emo track of all time".