The 43-year-old comedian will host the "58th Annual Primetime Emmy Awards" on Aug. 27. The show will air live from the Shrine Auditorium on NBC.
O'Brien hosted the Emmys in 2002 and did "a tremendous job," Dick Askin, chairman of the Academy of Television Arts & Sciences, said Friday. "We're thrilled that he's returning."
O'Brien, host of NBC's "Late Night With Conan O'Brien" since 1993, will take over the "Tonight" show from host Jay Leno in 2009.
His nightly hosting duties make O'Brien an ideal choice for the prime-time special, said Jeff Ross, producer of "Late Night" and co-producer of the Emmy Awards.
"When you've done 2,300-plus hours of television in front of a live audience and you do it well, it equips you for the role of playing the host," Ross said.
Emmy co-producer Ken Ehrlich called O'Brien "a student of television" who will bring "credibility and knowledge" to the show.
"He's funny and he really likes television," Ehrlich said. "That bodes well for what we can do this year."