The warrant was issued late yesterday, said a spokeswoman at Sweden's prosecutors' office in Stockholm.
She said Assange should contact the Swedish police for questioning about the accusations of molestation and rape in two separate cases "so that he can be confronted with the suspicions".
Assange has denied the charges, which were first reported by the Swedish tabloid Expressen, on Wikileaks' Twitter account.
He implied that they were linked to the release by the whistleblowers' website of a huge cache of US military records about the Afghan war, which were published in collaboration with the Guardian and two other newspapers.
Assange wrote: "The charges are without basis and their issue at this moment is deeply disturbing."
Earlier postings on the Twitter account implied the accusations were part of a dirty tricks campaign against the Wikileaks founder, who has been strongly criticised by the Pentagon.
"Expressen is a tabloid; No one here has been contacted by Swedish police. Needless to say, this will prove hugely distracting.
"We were warned to expect 'dirty tricks'. Now we have the first one."
Last month Wikileaks released around 77,000 secret US military documents on the war in Afghanistan.
US authorities criticised the leak, saying it could put the lives of Nato troops and Afghan informants at risk.