A CW representative, whose name was not reported, confirmed Whedon's announcement Friday to The Hollywood Reporter, though an air date has yet to be determined.
Whedon and his brothers, Jed and Zack, created the musical, starring Neil Patrick Harris, Nathan Fillion and Felicia Day, during the 2008 writers' strike as a way to avoid using the studio system. The three handled every aspect of production on the film, including distribution and marketing, and released it on iTunes.
The 45-minute film debuted at Comic-Con that year and has been a staple at the convention ever since.
"Dr. Horrible" won the Creative Arts Emmy for outstanding special class short-form program in 2009.
Members of Congress to keep receiving porn magazine
Putin thinks Obama would save him if he were drowning