Twenty-five people were arrested after violence broke out between police and demonstrators who pelted officers with placards as they tried to breach a police cordon set up near the prime minister's Downing Street residence.
Police officers were seen beating protesters with batons.
'Illegal war'
Bush is on what is expected to be his final European tour as US president before he steps down in January.
"This is also a signal to the incoming president that the people of this country are absolutely against this illegal war and destroying civil liberties," said Sarah Cox, a 71-year-old retired teacher who carried a Bush effigy bearing a cowboy hat, toy pistol, and miniature missile.
Security was tight with London's Metropolitan Police saying they had deployed about 1,200 officers to secure the president's 24-hour visit to Britain.
It is the first time Brown is hosting
Bush on home soil [AFP]
It is the first time Brown, who took over from Bush's close political friend, Tony Blair, has hosted him on home soil.
The leaders are expected to hold talks on Iran amid speculation of a growing rift over the deployment of British troops in Iraq.
A report in The Observer newspaper in Britain suggested Bush would warn Brown against a premature withdrawal from Iraq.
Bush said in an interview with the newspaper that "no definitive timetable" should be given for pulling out troops from Iraq, in what the paper had described as a "warning" for Brown.
Stephen Hadley, the US national security adviser, dismissed the report saying "there is no disagreement between us, between the president and prime minister Brown, on this issue, period".
The two leaders agree that any withdrawal "has to be a result of progress on the ground, on the advice of our military, and not according to any arbitrary schedule", Hadley added.
Another US official branded the report "ludicrous".
Both sides said the talks would include climate change, the state of the global economy and ongoing efforts to agree an international "trade liberalisation" deal.
Bush is scheduled to head to Northern Ireland on Monday, his last stop before flying home.