The 47-year-old Wikileaks founder also faces a separate hearing on 2 May over a request from the United States for his extradition for alleged computer hacking.
Assange was taken into custody after officials invited police officers into the Ecuador embassy where Assange had sought asylum.
US authorities had until Thursday refused to confirm reports that they had issued a sealed indictment against Assange.
The US Justice Department said Assange was being charged with a computer hacking conspiracy relating to his work in March 2010 with the former US intelligence analyst Chelsea Manning.
"Assange is charged with conspiracy to commit computer intrusion and is presumed innocent unless and until proven guilty beyond a reasonable doubt," a US Justice Department statement said. "If convicted, he faces a maximum penalty of five years in prison."
Assange will now be at the heart of a legal and diplomatic tug of war pitting him and his legions of supporters against the US justice system.
Speaking outside Westminster magistrates' court, Assange's lawyer, Jennifer Robinson, said: “Since 2010 we’ve warned that Julian Assange would face prosecution and extradition to the United States for his publishing activities with Wikileaks. Unfortunately today we’ve been proven right.
“This sets a dangerous precedent for all media organisations and journalists in Europe and elsewhere around the world.
"This precedent means that any journalist can be extradited for prosecution in the United States for having published truthful information about the United States.”
Sajid Javid, the British interior minister, told MPs: “Ecuador’s actions recognise that the UK criminal justice system is one in which rights are protected and in which, contrary to what Mr Assange and his supporters claim, he and his legitimate interests will be protected.”
Javid said that full extradition papers would need to be received by a judge within 65 days and then passed on to the British government for certification.