"In the interest of both parties in seeing this matter resolved, a mutually satisfactory settlement has been reached today," the UN refugee agency and former senior investigator, Caroline Hunt-Matthes, said in a joint statement.
No details of the deal were revealed, but UNHCR said it "accepts there were matters which in hindsight could have been better managed in relation to the separation."
Hunt-Matthes told AFP her contract with UNHCR was terminated after she raised concerns in 2003 over the way investigations of suspected sexual assault and rape cases were handled.
Huge congratulations to Caroline Hunt-Matthes who never gave up and pursued justice for 15 years.— Lori Handrahan (@LoriHandrahan2) June 5, 2018
UNHCR finally did the right thing.
Caroline paved the way for others to experience justice.
Thank you Caroline!#AidToo#MeToo#TimesUp https://t.co/LKTtTjtR3g pic.twitter.com/Vh0XgWZPLF
According to the Government Accountability Project (GAP), an NGO that supports whistleblowers, the "15-year retaliation case (is) the longest in the history of the United Nations internal justice system."
The settlement comes as the UN, like other institutions, is caught up in a global reckoning over sexual misconduct, spurred by the #Metoo movement.
UN Secretary-General António Guterres, who was head of UNHCR at the time Hunt-Matthes was fired, recently reiterated the world body's "zero tolerance" towards sexual abuse, and vowed to do more to investigate and to ensure accountability.
Hunt-Matthes first challenged UNHCR over sexual assault probes after she was deployed to Sri Lanka in October 2003 to follow up on a rape investigation initially handled by a senior manager on site.
The alleged victim, a refugee hired to work as a UNHCR cleaner, had been fired while the alleged rapist, a local UNHCR staff member, was transferred.
Hunt-Matthes, today an adjunct professor in Geneva and Grenoble, says she faced "unprecedented obstruction of the rape investigation, both before, during and after."
Her probe did eventually lead to the firing of the alleged rapist. UNHCR told AFP he was "summarily dismissed" on September 1st, 2004.
But a month prior to that, Hunt-Matthes herself was let go after she criticised the lack of independence.
She said UNHCR sent her an email saying her fixed-term appointment was terminated while she was in hospital recovering from a work-related car accident.
The documentation justifying her dismissal, a poor performance report, was drawn up after she was let go, she said.
A ruling by the United Nations Dispute Tribunal in 2013 found that Hunt-Matthes's firing was an act "of retaliation against her for questioning the (agency's) investigation methods ... and requiring investigations into the conduct of some senior officials."
The UNHCR appealed that ruling in 2014, and that new case was finally settled Monday.
UNHCR spokeswoman Cecile Pouilly told AFP that while the agency acknowledged it could have handled matters better, "there has been no legal finding that the non-renewal of Ms. Hunt-Matthes' contract was retaliatory."
But the former investigator stressed that UNHCR's appeal was "on a technicality (and) doesn't change the substance" of the prior court ruling that her firing was "retaliation".
"My case illustrates that every UN internal recourse for justice and whistleblower protection failed," she said.
She especially slammed the UN's continued use of internal investigation procedures.
"You can't be a party to a system and the judge," Hunt-Matthes said, calling for "true independence and neutrality."
Hunt-Matthes said she had settled "because 15 years is too long for anybody."
"I feel an enormous sense of relief that this is finally over."