House of Cards will contend against Breaking Bad, Downtown Abbey, Game of Thrones, Homeland and Mad Men in the category.
House of Cards was not the only online series nominated for an Emmy. Netflix's Arrested Development and The Newsroom actors are up for performance awards.
Kevin Spacey from House of Cards and Jeff Daniels from The Newsroom are both nominated for best actor in a drama series.
House of Cards' Robin Wright is nominated for best actress in a drama series.
In the comedy series category, Arrested Development's Jason Bateman is nominated for best actor.
The most Emmy nominations, 17, went to American Horror Story: Asylum. Close behind was Game of Thrones with 16 nods, while Saturday Night Live and the Liberace biopic Behind the Candelabra earned 15 nominations each, including nods for stars Michael Douglas and Matt Damon.
Breaking Bad's Paul and How I Met Your Mother's Harris announced this year's Emmy Award nominees, which celebrate daytime television achievements.
Both emcees were themselves nominated for an Emmy. Paul is up for best supporting actor in a drama series, while Harris is up for his role as a producer for another awards show.
Harris, the host of this year's celebration of daytime television, was a last-minute addition to the nomination announcement. Kate Mara, from Netlix's House of Cards, was to co-host the announcement. Her flight had mechanical issues Wednesday night, and she was unable to make it.
Harris thanked Mara for getting him out of the house before his twins woke up and started crying.
Acting nominations include:
Best actress in a drama series: Vera Farmiga, Bates Motel; Michelle Dockery, Downtown Abbey; Claire Danes, Homeland; Robin Wright, House of Cards; Elisabeth Moss, Mad Men; and Connie Britton, Nashville.
Best actor in a drama series: Bryan Cranston, Breaking Bad; Hugh Bonneville, Downtown Abbey; Damien Lewis, Homeland; Kevin Spacey, House of Cards; Jon Hamm, Mad Men; and Jeff Daniels, The Newsroom.
Best supporting actress in a drama series: Anna Gunn, Breaking Bad; Maggie Smith, Downtown Abbey; Emilia Clarke, Game of Thrones; Morena Baccarin, Homeland; Christina Hendricks, Mad Men; and Christina Baranski, The Good Wife.
Best supporting actor in a drama series: Bobby Cannavale, Boardwalk Empire; Jonathan Banks, Breaking Bad; Aaron Paul, Breaking Bad; Jim Carter, Downtown Abbey; Peter Dinklage, Game of Thrones; and Mandy Patinkin, Homeland.
Best actress in a comedy series: Tina Fey, 30 Rock; Laura Dern, Englightened; Lena Dunham, Girls; Edie Falco, Nurse Jackie; Amy Poehler, Parks and Recreation; and Julia Louis-Dreyfus, Veep.
Best actor in a comedy series: Alec Baldwin, 30 Rock; Jason Batemen, Arrested Development; Matt LeBlanc, Episodes; Don Cheadle, House of Lies; Louis C.K., Louie; and Jim Parsons, The Big Bang Theory.
Best supporting actress in a comedy series: Jane Krakowski, 30 Rock; Jane Lynch, Glee; Sofia Vergara, Modern Family; Julie Bowen, Modern Family; Marritt Wever, Nurse Jackie; Mayim Bialik, The Big Bang Theory; and Anna Chlumsky, Veep.
Best supporting actor in a comedy series: Adam Driver, Girls; Jesse Tyler Ferguson, Modern Family; Ed O'Neill, Modern Family; Bill Hader, Saturday Night Live; and Tony Hale, Veep.
The awards ceremony will air Sept. 22.