The series was greenlit after Viacom bought the complete rights to the Teenage Mutant Ninja Turtles franchise from creator Peter Laird for $60 million in October 2009, with the announcement also confirming a companion live-action feature film for Paramount Pictures.

The show was developed simultaneously with a revamped Winx Club series at Nickelodeon Animation Studio as part of a strategy to reboot two established brands, one targeting boys aged 6 to 11 and the other targeting girls of a similar age.

Creative team members had different influences: designer Ciro Nieli drew on the original 1984 comics, while writers Jennifer Ventimilia and Joshua Sternin were fans of the 1987 animated series and the 1990s live-action films during college.

Leonardo's original voice actor Jason Biggs was replaced partway through season 2 by Dominic Catrambone for the last seven episodes, before Seth Green took over the role permanently starting in season 3, announced in June 2014.

Rob Paulsen, who voices Donatello in this series, had previously voiced Raphael in the 1987 TMNT animated series.

Corey Feldman, who voiced Donatello in the first and third live-action TMNT films, was cast to voice the character Slash in this series.

Comedian Roseanne Barr voiced the villain Kraang Prime in seasons 1 and 2 before being replaced by Rachel Butera in season 3.

The series featured crossovers with the 1987–1996 TMNT animated series reality, including appearances by that era's Turtles, Bebop, Rocksteady, and Krang, an exiled relative of this show's Kraang Subprime.

The two-part series premiere in September 2012 drew 3.9 million viewers, marking the highest debut ratings for a Nickelodeon animated series since 2009 and leading to an immediate second-season renewal.

Executive producer Ciro Nieli stated he wanted the TV film 'Raphael: Mutant Apocalypse' to serve as the definitive series finale specifically to prevent any future alteration of the show's established timeline.