"Buckle your seat belts, Emmy viewers!" said Samberg in a statement, promising viewers "a wild ride".
The Brooklyn Nine-Nine star will host the ceremony in Los Angeles on 20 September.
Samberg performed on SNL for seven seasons, before joining police sitcom Brooklyn Nine-Nine in which he plays Detective Jake Peralta.
The role earned him a Golden Globe for best comedy actor last year.
"Buckle your seat belts, Emmy viewers! Like, in general you should buckle your seat belts in your car. In fact, even if you're not an Emmy viewer, you should buckle your seat belt. It can be dangerous on the road," Samberg quipped, in a statement
"Also, if you're not an Emmy viewer, you should strongly consider becoming one this year, because I'm hosting, and it's gonna be a wild ride."
The 36-year-old previously won an Emmy in 2007 for a sketch song he performed on SNL, as part of the comedy troupe The Lonely Island.
The song - sometimes known as "Special Treat in a Box" - won Samberg and collaborator Justin Timberlake the Emmy for outstanding original music and lyrics after it became a major viral hit.
Fearless
As The Lonely Island, Samberg also performed on Everything is Awesome, the hit song from The Lego Movie.
Fox TV's Gary Newman and Dana Walden - who will broadcast the live ceremony - said this year's host "had to be Andy".
"He is fearless, hilarious, an award-winning comedian, singer, writer and actor with incredible live TV experience. We know he'll deliver the laughs and give viewers an incredible night."
Last month, the Television Academy announced new rules for the Emmy Awards.
Among the changes will be an increase to the number of nominees in comedy and drama categories, from six to seven.
Comedy series must now run for half an hour, or less, per episode, while drama series must run for more than 30 minutes per episode.
The award for mini-series was renamed as limited series.
Andy Samberg, best known for Saturday Night Live, will host this year's Primetime Emmy Awards.