Since the end of his creator-owned teen drama series The Waiting Place, which was published from 1997 to 2002, he has written several series for Marvel Comics, including The Incredible Hulk, Sentinel, Mary Jane, Inhumans and Gravity.
In 2005, he won an Eisner Award for Talent Deserving of Wider Recognition.
He has written for the monthly comic books Gravity, Marvel Adventures Spider-Man, Sentinel and Spider-Man Loves Mary Jane, all for Marvel Comics, and on January 9, 2007, DC Comics announced that McKeever had signed an exclusive contract with the publisher. He was a part of the writing team working on DC's weekly series Countdown, and took over for Gail Simone as the writer of Birds of Prey after issue #112, however, his last issue was #117 due to time constraints with deadlines. Sean also took up writing duties on Teen Titans with the double sized August issue #50 and also wrote the Terror Titans limited series that spun off from this. His run on Teen Titans has ended with issue #71, although he has continued with a Ravager back-up story starting in #72.
It was announced at Wizard World Philadelphia 2009 that McKeever, no longer under exclusive contract to DC, would write the limited series Girl Without a World for Marvel Comics and this led into Young Allies a new series and team formed after the Heroic Age line-wide reboot, all with artist David Baldeon.
McKeever is also wrote a new story for The Waiting Place illustrated by Mike Norton. The story was printed in The Waiting Place: The Definitive Edition from IDW Publishing.