It was issued in 2012 for jumping bail.
Senior District Judge Emma Arbuthnot said at Westminster Magistrates' Court on Tuesday that she was not persuaded that the warrant should be withdrawn, despite the argument he still has no goal. However, Assange will be able to appeal against the decision.
Sweden dropped its investigation a year ago, but British police are still seeking to arrest Assange for failing to surrender to a court after violating bail terms during his unsuccessful battle against extradition.
However, a judge at Westminster Magistrates Court said it remained valid because he had committed an offence by skipping bail in June 2012 - when he first took refuge in the Ecuadorian embassy in London.
The judge said that if Assange wanted the warrant lifted he should surrender to authorities and come to court.
After the ruling keeping the warrant in place, the judge agreed to let Assange's lawyer, Mark Summers, argue in his client's absence that the warrant should be lifted because it was no longer in the public interest to arrest Assange.
"[Assange] has spent five-and-a-half years in conditions which, on any view, are akin to imprisonment, without access to adequate medical care or sunlight, in circumstances where his physical and psychological health have deteriorated and are in serious peril", Summers wrote in court papers, as quoted by the Guardian.
In 2016, a United Nations panel said that Sweden and the U.K. were arbitrarily detaining Assange, NPR's Leila Fadel reported.
Arbuthnot said she would rule on those arguments February 13.
Still, Assange has been unable to leave the embassy in London, as he faced arrest for breaching his bail conditions in the UK.
Mr Assange came to global prominence in 2010 when his website Wikileaks released tens of thousands of classified military and diplomatic documents.
It is not publicly known whether there is a sealed USA indictment against Assange.
There are no formal charges in against Assange in the USA, though news reports a year ago suggested the Justice Department was looking into it.
US officials haven't confirmed whether a request for Assange's extradition has been made.
Assange was made an Ecuadorian citizen in December.
Ecuador also asked Britain to grant him diplomatic status. Sweden dropped its case after deciding there was no reasonable hope of bringing Assange to Sweden to answer questions.
"In order to proceed with the case, Julian Assange would have to be formally notified of the criminal suspicions against him".
However, Metropolitan Police in London said Mr Assange will still be arrested - for failing to surrender to a court - if he leaves the embassy.