"It's hard to tell how big the crowd is because there are a lot of people who are more spectators than demonstrators in the plaza," David Hawkins, Al Jazeera's correspondent, reported from Seoul.
Close by, a separate rally advocating closer US-South Korea ties also took place.
"There was a much larger demonstration just down the road earlier in the day by people who were welcoming George Bush on his visit to Seoul," Hawkins said.
Bush missed both protests, arriving at a military airport south of the capital and then being driven to a hotel after a welcoming ceremony including a 21-gun salute.
Lee's government faced mass protests earlier in the year after it lifted an embargo on US beef imports introduced in 2003 after a case of mad cow disease was diagnosed in the US.
The protests abated after Seoul won some promises of safeguards from Washington such as pledges that meat from older cattle would not be exported to South Korea.
US beef imports resumed on July 29, although many larger South Korean shops and restaurants still refuse to serve the meat.
In addition to the recent controversy over South Korea's imports of US beef, Bush and Lee are expected to discuss efforts to end North Korea's nuclear weapons drive.
On leaving South Korea, Bush will visit Thailand where he is expected to deliver a foreign policy speech and to condemn the military government of Myanmar, formerly known as Burma, for human rights abuses.
Bush will then head to China to attend the opening ceremony of the Beijing Olympics.
Rights activists and some US politicians have called for Bush to boycott the games over human rights concerns.
But Bush said last week that the Olympics was not a place for political statements and that not attending would offend the Chinese people.
"I made a decision not to politicise the games; this is for athletics," he said.
"There's plenty of time for politics, and I'm confident I'll have time for politics."