The former Thunderbolts writer will join the series for a six-issue run following the conclusion of Nick Spencer and Scot Eaton's Fear Itself tie-in arc.
Ellis's run on the title will consist of six single-issue adventures, rather than the usual form of an extended six-issue story arc.
"I like the idea of there being a few books out there that don't require you to commit to buying another five issues to find out how the story ends," Ellis told Marvel.
Tom Brevoort, Marvel Comics SVP of publishing, added: "In Warren's run, each issue will be a high octane adventure, hyper-compressed into a single instalment."
A different artist will pencil each individual issue of Ellis's run, beginning with Phonogram artist Jamie McKelvie.
The writer will focus on a different set of team members in each issue, beginning with a story featuring Steve Rogers, Black Widow, Moon Knight, and Beast.
Ellis received critical acclaim for his run on the supervillain series Thunderbolts, as well as his recent work on Astonishing X-Men.
Ellis begins his run with Secret Avengers #16 this July.