Frank Friel, director of security at the Independence Visitor Center, made the official estimate.
The crowd exceed the 30,000 who greeted Obama and Oprah Winfrey in December in Columbia, S.C.
Obama told the crowd the United States is at a crucial moment in its history, much like what the founding fathers faced in Philadelphia.
"It was over 200 years ago that a group of patriots gathered in this city to do something that no one in the world believed they could do," Obama said. "After years of a government that didn't listen to them, or speak for them, or represent their hopes and their dreams, a few humble colonists came to Philadelphia to declare their independence from the tyranny of the British throne."
The Illinois senator called Democratic rival Hillary Rodham Clinton a "tenacious" opponent but said it was time to move beyond the politics of the 1990s.
"Her message comes down to this: We can't really change the say-anything, do-anything, special interest-driven game in Washington, so we might as well choose a candidate who really knows how to play it," Obama said.
