Creators Brad Wright and Robert C. Cooper conceived Stargate Universe as a completely separate third entity in the franchise, distinct from Stargate Atlantis which had been a spin-off of Stargate SG-1.

Wright and Cooper originally planned to write the pilot script during summer 2007, aiming for a 2008 premiere, but the project was put on hold due to ongoing work on Stargate Atlantis and Continuum, plus the 2007-2008 Writers Guild of America strike.

The series was officially greenlit for a 2009 debut on August 22, 2008, shortly after the cancellation of Stargate Atlantis was announced, and producer Joseph Mallozzi noted the new series would have lower salaries and licensing fees than a sixth season of Atlantis would have had.

Character breakdowns for casting calls leaked online in September 2008 under different working names for the characters, including Eli Wallace as 'Eli Hitchcock', Matthew Scott as 'Jared Nash', and Ronald Greer as 'Ron "Psycho" Stasiak'.

Robert Carlyle kept his Scottish accent for the role of Nicholas Rush but mixed it with an English accent.

Ming-Na Wen's character Camile Wray is the first openly lesbian character in the Stargate franchise.

Most of the Stargate Atlantis crew moved over to Universe, including stunt coordinator James Bamford and composer Joel Goldsmith.

The episode 'Air (Part 3)' was filmed on location in and around Alamogordo, New Mexico from late April through early May 2009, while the rest of the show was shot at The Bridge Studios in Vancouver.

Stargate Universe adopted a markedly different, more documentary-style shooting approach for greater realism and immediacy, drawing inspiration from the film Cloverfield.

The episode 'Time' won a Writers Guild of Canada Award for best one-hour TV series, and Robert Carlyle won Best Performance by an Actor in a Continuing Leading Dramatic Role at the 2010 Gemini Awards for the episode 'Human'.

Both 'Air' and 'Space' were nominated for Outstanding Special Visual Effects For A Series at the 2010 Primetime Emmy Awards.

Syfy cancelled the series after its second season, and co-creator Brad Wright attributed declining ratings partly to the show being moved from its Friday timeslot to Tuesday and then Monday, as well as to some angry SG-1 and Atlantis fans deliberately hurting viewership.