After recording their twentieth anniversary concert, Score, on April 1, 2006, Dream Theater rested for its first summer in ten years. The band would reconvene at Avatar Studios, in New York City, in September 2006. Mike Portnoy stated that the relationship between band members was "the best it's ever been". The band hired Paul Northfield, who had previously worked with bands that had inspired Dream Theater, including Rush and Queensrÿche, to engineer the album. As with previous albums, Dream Theater simultaneously wrote and recorded Systematic Chaos. Mike Portnoy and John Petrucci co-produced the album; Portnoy said that the band hires an engineer and a mixer to act as an "objective outside ear", but the members ultimately "call their own shots". Previous Dream Theater albums shared planned themes throughout, such as Metropolis Pt. 2: Scenes from a Memory (1999) as a concept album or Train of Thought (2003) as a heavy, "balls to the wall" album. Though Portnoy had some preconceived ideas for Systematic Chaos, he decided not to tell the rest of the band; leaving them to start with a "completely open palate". However, Portnoy did want to retain a "cutting, aggressive, modern" mood throughout, "It had to have balls," he added, "it had to be cool".

The album was titled Systematic Chaos after Portnoy and Petrucci picked phrases from song lyrics that they felt would be a fitting title, in similar fashion to previous albums like Images and Words (1992) or Awake (1994). The pair selected the word "chaos", which appears in "The Dark Eternal Night". Petrucci and Portnoy were also attracted to the phrase "Random thoughts of neat disorder" which appears in "Constant Motion". Inspired by the "duality" of the phrase, opposites of the word "chaos" were discussed, resulting in the word "systematic". Portnoy said that in addition to the album, "systematic chaos" is also a "fitting description of the band in general".