Shortly before the US president met Mr Brown, hundreds of demonstrators gathered in Parliament Square to shout: "George Bush - terrorist".
The protest rally was organised by the Stop War Coalition, CND and the British Muslim Initiative.
The demonstrators had planned to march to Downing Street, but police closed down Whitehall and used heavy reinforcements to ensure the metal barrier they erected was not breached.
Police said at least 10 officers received minor injuries, and 25 people were arrested.
Andrew Burgin, a spokesman for the coalition, which earlier staged a small demonstration outside Windsor Castle, said: "We think Bush is a war criminal. Both Blair and Bush are responsible by duplicity and lying for an illegal invasion of Iraq."
Cakes and sandwiches
Mr Bush's 45-minute tea meeting with the Queen was billed by Buckingham Palace as a "private and informal" visit between "old friends".
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