Flying Lotus has released four studio albums—1983 (2006), Los Angeles (2008), Cosmogramma (2010), and Until the Quiet Comes (2012)—all to increasing critical acclaim. He has produced much of the bumper music on Cartoon Network's Adult Swim programming block. He also contributed remixes for fellow Plug Research artists including Mia Doi Todd. He is often referred to as FlyLo by fans and critics.

In 2012, Ellison began rapping under the persona Captain Murphy. Ellison kept the fact that he was Captain Murphy a secret for several months, finally revealing it several weeks after the release of his first rap mixtape, Duality.

In 2007, Flying Lotus announced that he signed with Warp Records. Following his Warp debut, the six-track Reset EP, he quickly became one of the label's cornerstone artists and released his second album, titled Los Angeles, on June 10, 2008. The same year, Flying Lotus also remixed "Reckoner" from Radiohead's album In Rainbows. His third album, Cosmogramma, was released in the UK on May 3, 2010, and in the US on May 4, 2010. In January 2011, Cosmogramma won in the Dance/Electronica Album category in the 10th Annual Independent Music Awards.

In 2010, Flying Lotus collaborated with the Ann Arbor Film Festival in the performance of a live scoring of the 1962 avant-garde film Heaven and Earth Magic. In a post-viewing interview with the audience, Flying Lotus said that he was unsure whether or not a recording of the performance (or a recreation of it) would be publicly released, but he would be enthusiastic toward similar projects in the future. He was chosen by Battles to perform at the ATP Nightmare Before Christmas festival that it co-curated in December 2011 in Minehead, England, UK.

In January 2011, Flying Lotus won the 10th Annual Independent Music Awards for his video "MmmHmm" in the Short-Form Video category. In August 2011, Flying Lotus announced a multimedia project with filmmaker Miwa Matreyek, which is to be titled The Mapping of Countries Yet to Come.

Flying Lotus produced rapper Mac Miller's song “SDS’” for his album Watching Movies with the Sound Off. He also created a song for the Cartoon Network series Adventure Time entitled “About that time//A glitch is a glitch”.

It was reported in 2011 that Flying Lotus would be collaborating with R&B singer Erykah Badu on new material for her next album, and planned to remix one of Radiohead's songs from The King of Limbs.

In April 2013, Flying Lotus announced that he would be getting his own radio station in the upcoming video game Grand Theft Auto V, saying there would be "a ton of new songs and information, including rapping a new Captain Murphy song produced by Hudson Mohawke".