Bosses at the firm, which launched a Tv and film studio wing in 2010, have ordered a pilot of Carter's post-apocalyptic drama The After.
The project will mark the first time Carter has worked on a Tv pilot since his X-Files spin-off The Lone Gunmen, which ran for one series in 2001.
The show will be streamed online. Amazon Studios is also working on projects with John Goodman and Jeffrey Tambor.
Carter penned The X-Files from 1993 until 2002, before writing the big screen spin-offs in 1998 and 2008.