In the hiatus, the members undertook side projects, with MacKaye forming the duo the Evens with drummer and singer Amy Farina (formerly of the Warmers).
In 2004, MacKaye produced the DC EP for Red Hot Chili Peppers guitarist John Frusciante, which also featured Jerry Busher.
Canty has been doing a variety of soundtrack scores and playing bass in the trio Garland Of Hours alongside frequent Fugazi guest contributors Jerry Busher and Amy Domingues, and has played bass live with Mary Timony. Canty also appears on Bob Mould's 2005 album, Body of Song, and on Mould's 2008 album, District Line, and has toured with Mould, appearing in the live DVD, Circle of Friends. He is currently working in the Burn to Shine DVD series which is being released by Trixie DVD. Now, he is playing in Deathfix alongside Devin Ocampo (Medications, Faraquet, Smart Went Crazy, Beauty Pill), Rich Morel (Bob Mould, Blow Off), and Mark Cisneros (Medications, the Make-Up). They released their album in February 2013 on Dischord Records.
Lally has released three solo albums, There to Here (2006), Nothing Is Underrated (2007), and Why Should I Get Used to It (2011). He has also appeared on fellow DC post-punkers Decahedron's debut album, Disconnection_Imminent, as well as on a project with Red Hot Chili Peppers guitarists John Frusciante and Josh Klinghoffer, known as Ataxia. The group has recorded two albums, Automatic Writing (2004) and AW II (2007).
Picciotto currently works as a record producer most notably with Blonde Redhead and the Blood Brothers, and he has performed alongside members of the Ex at the Jazz festival in Wels, Austria. Picciotto also contributed guitar on two Vic Chesnutt albums, 2007's North Star Deserter and 2009's At the Cut (co-producing the latter), for Constellation Records, and performed live with Chesnutt and members of Thee Silver Mount Zion Memorial Orchestra and the Quavers in Jem Cohen's program entitled "Evening's Civil Twilight in Empires of Tin at the Vienna International Film Festival (Viennale) in 2007 (a DVD of the program was released in 2009). Picciotto played guitar on Chesnutt's Fall/Winter 2009 North American Tour. He's also worked as a producer for the project Xylouris White, and is considered by the members to be a "non-performing" member.
In July 2011, Minneapolis based record label Doomtree released an album of mash-ups between Fugazi and east coast veteran rap crew the Wu-Tang Clan. The album is titled 13 Chambers and the group's name is Wugazi. However, Fugazi itself did not have any involvement with the release. Bassist Joe Lally was asked about his thoughts on the Wugazi release, and stated "I think they could've found better Fugazi pieces to sample with Wu-Tang guys rapping on it. I mean, it's enjoyable, and I do appreciate it for the fact that somebody enjoys our music enough to bring it into that. But, you know, I don't know. I guess I should shut up, because I suppose I'm about to run into these people at the Fun Fun Fun Fest festival and talk to them. But I'm afraid that is my opinion on it. It's like, get better samples of our stuff, do better work."
In October 2012, Chris Lawhorn released Fugazi Edits. The album includes 22 instrumental tracks, which sample 100 songs from Fugazi's discography. As in other cases, the band had no involvement in the album's production, but it was authorized for release by MacKaye, with the proceeds going to charity.
In 2013, Brendan Canty released a collaborative album along Rich Morel under the name Deathfix and toured briefly from 2012 to 2014. In 2016, Canty and Lally joined with guitarist Anthony Pirog to form the Messthetics, Canty and Lally's first project together since Fugazi's hiatus. In March 2018, the Messthetics released their self-titled debut album and embarked upon a tour in the US and Japan. The band toured further and released a second album entitled Anthropocosmic Nest in 2019.
In 2018, Ian MacKaye, Amy Farina and Joe Lally debuted a new band. In February 2020, it was announced that the band, now called Coriky, would release their first album on March 27, 2020. The debut single, "Clean Kill", was released on February 11, 2020. The band previewed their album at a free show in D.C.'s St. Stephen and the Incarnation Episcopal Church on February 22, 2020. Due to the COVID-19 pandemic, the release of Coriky's self-titled album was delayed to June 12, 2020, in part to accommodate independent record stores closed due to the pandemic. Upon release the record was favorably reviewed in a few publications; often drawing comparisons and contrasts with MacKaye and Farina's other band the Evens, as well as Fugazi.