Spotlight won in the Nations and Regions category for the programme Spotlight: A Woman Alone With The IRA.
The award was accepted by reporter Jennifer O'Leary at a ceremony in London on Thursday night.
The programme investigated the republican movement's handling of sexual abuse allegations.
Maíria Cahill waived her right to anonymity to talk to Spotlight.
The programme was broadcast in October 2014.
It won Scoop of the Year at the Royal Television Society (RTS) journalism awards in February.
Speaking on Thursday night, Jeremy Adams, head of television current affairs at BBC Northern Ireland, said: "This programme highlighted the plight of a young woman subjected to a kangaroo court by the IRA and made to confront an individual she accuses of raping her.
"The team put a great deal of time and dedication into what was a painstaking investigation to help expose a shocking abuse of human rights."
BBC Northern Ireland's current affairs programme Spotlight has won a UK-wide award at the prestigious Amnesty International Media Awards.