"By stepping down, President Mubarak responded to the Egyptian people's hunger for change," Obama said from Grand Foyer of the White House on Friday. "But this is not the end of Egypt's transition. It's a beginning."
The resignation ended a period of tension and uncertainty for the Obama administration, which had expected that Mubarak would announce his resignation during a television appearance from Egypt on Thursday night.
That departure instead was announced Friday, after throngs of Egyptians gathered outside the presidential palace in Cairo.
The Egyptian military will now take control of the government and it is unclear whether Egyptian Vice President Omar Sulieman will retain any power.
"The military has served patriotically and responsibly as a caretaker to the state, and will now have to ensure a transition that is credible in the eyes of the Egyptian people," Obama said.
Obama clarified that a "credible" transition would mean an end to the 30-year-old emergency laws that give police broad powers during protests, and changes to Egypt's constitution to ensure fair elections.
"There will be difficult days ahead," Obama said.
When asked about the uncertainty of the transition, White House press secretary Robert Gibbs said, "I don't think we have to fear democracy."
Gibbs said the U.S. will play a "constructive role" in the transition.
"We will continue to be involved," he said following Obama's remarks.
He deflected further questions concerning the president's specific plans, but appeared eager to offer the administration's outlook on the possibility of anti-government protests erupting in Iran.
"There is quite a contrast between Iran and Egypt," he said, calling Iranian President Mahmoud Ahmadinejad's government "scared" for threatening to kill dissenters.
Gibbs suggested he wouldn't be surprised if Iran's government was the next toppled in the Middle East, saying the Iranian government is afraid of "the will of its people."