Covert Affairs first appeared on USA Network's development slate in July 2008, with the pilot episode written by Matt Corman and Chris Ord.

Piper Perabo was the first actress cast in early July 2009 as CIA officer Annie Walker, followed by the casting of Christopher Gorham in late July, which was quickly followed by USA Network green-lighting the pilot.

Eric Lively was originally cast as a fellow CIA officer and peer to Perabo's character, but after the pilot received a 10-episode order in January 2010, his role was replaced by Sendhil Ramamurthy's character Jai Wilcox.

The series is filmed in Toronto, Ontario, using primary static sets in a studio combined with 'stock' shooting locations throughout the local area to stand in for international settings like Washington, D.C.

Producers sometimes used stand-in locations for shots when the costs and logistics of filming at the actual real-world location were impractical, or when the specified location was entirely fictional.

Tim Matheson signed on in early August 2009 to direct the 90-minute pilot, which began filming in Toronto in September 2009.

Piper Perabo was nominated for Best Performance by an Actress in a Television Series–Drama at the 68th Golden Globe Awards and won the Outstanding Female Actor in a Breakthrough Role award at the 2011 Gracie Awards.

Christopher Gorham, who played the blind character Auggie Anderson, won the Seeing Beyond Vision Loss Special Achievement Award at the 2013 CNIB Awards.