The Met Police said he was arrested for failing to surrender to the court and following a US extradition request.
Ecuador's president said it withdrew his asylum after repeated violations of international conventions.
"Julian Assange, 47, has today, Thursday 11 April, been arrested by officers from the Metropolitan Police Service (MPS) at the Embassy of Ecuador," police said.
Police said they arrested Assange after being "invited into the embassy by the Ambassador, following the Ecuadorean government's withdrawal of asylum."
The arrest marks the end of one of the most peculiar turns of Assange's tumultuous life, though his supporters said Ecuador's termination of his asylum was illegal and feared that Assange would end up in the United States.
Who is Julian Assange ?
Julian Assange is a valiant campaigner for truth. To his critics, he is a publicity-seeker who has endangered lives by putting a mass of sensitive information into the public domain.
Mr Assange is described by those who have worked with him as intense, driven and highly intelligent with an exceptional ability to crack computer codes.
He set up Wikileaks, which publishes confidential documents and images, in 2006, making headlines around the world in April 2010 when it released footage showing US soldiers shooting dead 18 civilians from a helicopter in Iraq.
But, later that year, he was detained in the UK - and later bailed - after Sweden issued an international arrest warrant over allegations of sexual assault.
Swedish authorities wanted to question him over claims that he had raped one woman and sexually molested and coerced another in August 2010, while on a visit to Stockholm to give a lecture.
He says both encounters were entirely consensual and a long legal battle ensued which saw him seek asylum in the Ecuadorean embassy in London to avoid extradition.