The minor was taken to hospital after being allegedly assaulted on September 30 in the southern town of Bambari, said UN spokesman Stephane Dujarric.
The UN said the girl was 16 years old, but Amnesty International, which interviewed her, said she was 19.
News of the allegation came as UN Secretary-General Antonio Guterres is preparing to meet victims of sex abuse by UN peacekeepers when he visits the Central African Republic later this month.
It will be the UN chief’s first visit to the poor African country struggling with sectarian violence since the 2013 overthrow of longtime leader Francois Bozize.
The United Nations has notified the country that sent the peacekeepers involved of the rape allegations and has requested that the government investigate, Dujarric said.
The country was not named, but UN sources said it was Mauritania.
Under UN rules, it is up to the country contributing troops to a peacekeeping mission to investigate and prosecute criminal cases.
Amnesty International said the victim told them that she had been drugged by the peacekeepers. They had given her tea when she approached them at a Bambari checkpoint after she became ill.
“She said she passed out not long after she drank the tea, and woke up on the ground nearby, several hours later, nearly nude,” an Amnesty statement read.
Guterres has made combating sexual abuse by UN peacekeepers a priority since taking over from Ban Ki-moon nine months ago.
The 12,000-strong MINUSCA force has been plagued by a wave of sexual abuse allegations since the mission to help restore stability to the country began in 2014.
In June, about 600 troops from Congo Republic who were serving in MINUSCA returned home following several allegations of sex abuse and other misconduct.
UN critics in the United States — many of whom are in the US Congress — point to the mounting cases of misconduct by UN peacekeepers to support their campaign to cut funding to peacekeeping.