Zuma lost his job in post-apartheid South Africa's most sensational corruption scandal in June, however denied corruption charges.
He has also strongly denied the rape allegations, after coming under pressure in the past fortnight amid reports of a police investigation.
"After due consideration of the facts in the relevant case docket the National Prosecuting Authority has decided that Mr Jacob Gedleyihlekisa Zuma be arraigned in the Johannesburg High Court on a charge of rape," a statement said.
"To this end Mr Zuma duly appeared in the Johannesburg Magistrate's Court today the 6th of December 2005, where the indictment and related documentation was served on him."
Zuma was released on 20,000 rand (A$4,250) bail and the trial date has been set for February 13.
No further details on the alleged rape have been disclosed.
Zuma remains the deputy leader of the governing ANC party but has faced increasing pressure to resign.
The party said it will issue a statement later on Tuesday.
President Thabo Mbeki fired Zuma in June after a court found his financial adviser guilty of corruption, and Zuma was charged with two graft counts shortly afterwards.
He is due to go on trial for corruption in July.