Before forming The Secret Machines the members played in various Dallas bands such as: UFOFU, Captain Audio, Comet and When Babies Eat Pennies, but perhaps the most significant was Tripping Daisy. Captain Audio was formed by Garza and vocalist/guitarist/chief songwriter Regina Chellew in the late 90s as a two-piece noise duo. Brandon — and occasionally Ben — Curtis joined shortly thereafter as the original duo began to head toward a more standard rock sound. In a few months the band was getting regular local press and within a little over a year they had recorded and released the EP My Ears Are Ringing But My Heart's OK (1999) and the full-length LUXURY or Whether It Is Better To Be Loved than Feared (2000) to positive reviews. Shortly after the release of LUXURY the band went on an extended hiatus and eventually disbanded when the boys headed for New York, leaving Chellew behind in Dallas to form the band Chao and later joining indie pop outfit The Happy Bullets.

Captain Audio is essentially the same band as the Secret Machines, with the exception of Chellew. Sonically the groups are very similar, much more so than any of the members' other former bands. Although Captain Audio is a bit more prone to experimentation and sound collage and the Secret Machines are much more a standard indie rock band, the Captain Audio records form the template that the Curtis brothers built upon when they headed for New York. In the liner notes for Captain Audio's LUXURY, all of the additional musicians who played on the album are credited simply as "Secret Machines".

The band went to Chicago first, where they recorded their EP, September 000, six weeks after forming, before continuing to New York. The EP didn't sell well, but remained a hit on indie radio while "Marconi's Radio" and "Breathe" are fan favourites.

In 2004, The Secret Machines released their first full length CD - Now Here Is Nowhere. Their second EP, The Road Leads Where It's Led, was released on 7 June 2005. The song "Nowhere Again", from the their debut album, was used in promotional spots for American during its launch, and appeared in the 2006 videogame Driver: Parallel Lines.

"Nowhere Again" is the band's biggest hit to date, being played at nearly every show since its conception.

Ten Silver Drops, their second album, leaked onto file sharing websites following the release of their lead single "Alone, Jealous and Stoned" in the UK.

The album once again did not sell well but garnered favorable reviews.

In 2006, the band did a headlining In-the-Round tour.

Benjamin Curtis left the band on March 3, 2007 to focus full time on his new band, School of Seven Bells. The news was posted by Brandon Curtis on the Secret Machines' messageboard.

After Ben's departure from the band, Secret Machines played two shows in New York, one at the Annex, and the other at the newly opened Highline Ballroom. At these shows, the band played mostly new material to be put on their next album. They included two new members: Blasco (Interpol's touring keyboardist) on guitar, keyboards, and bass, and ex-Tripping Daisy member Phil E. Karnats on guitar. Since these shows, Karnats has become the official guitarist of the band, replacing Ben.