"No, you don't run for second. I don't believe in that," Obama said on the "Late Show with David Letterman."
Letterman said Clinton and Obama would make a powerful team on the campaign trail.
"Which order are we talking about?" Obama asked, as the audience erupted in laughter.
Obama said he respected Clinton, calling her a "terrific senator."
"You know, I think all the candidates are in to win and one of the things about the process is, by the end of it, after having gone through all the debates and all the campaigning out in various states, people get a pretty good sense of who various candidates are and — but I think we're all on the same team," Obama said.
Obama defended his record in the Senate while on the campaign trail, saying he's only missed three votes.
"My staff is doing a terrific job making sure that we're tending to constituents back home, but I'm not getting back to Chicago very often, which — my wife is starting to refer to me as her first husband. It's a little disturbing," Obama said.