Samoura to take her post by mid-June after undergoing an eligibility check administered by an independent review committee.
Gianni Infantino promised a complete overhaul of FIFA when he took over as the tainted organisation's new president earlier this year. And the appointment of Fatma Samoura as the new secretary general is being widely seen as the first major step in the governing body's clean up act.
On Friday, Samoura, a UN diplomat from Senegal, became the first female and non-European secretary general of FIFA, in a move that Infantino said would bring "fresh winds" to the organisation.
"We have to be serious when we say we embrace diversity and we believe in gender equality," Infantino said, describing Samoura as the "most competent" person for the job, with experience in managing big organisations.
"She will bring a fresh wind to FIFA, somebody from outside, not somebody from inside, not somebody from the past, but somebody new."
Samoura, who has worked on humanitarian crises with the United Nations for 21 years, is currently based in Nigeria for the UN Development Programme.
The 54-year-old Senegalese, replaces Frenchman Jerome Valcke who was fired in January and has since been banned for 12 years over ethics violations, which included using FIFA expenses for sightseeing trips and destruction of evidence.
Samoura's appointment was suggested by Infantino and approved by the FIFA Council, but she will take her post by mid-June after undergoing an eligibility check administered by an independent review committee.
"Today is a wonderful day for me, and I am honoured to take on the role of FIFA's secretary general," Samoura, who has also worked at the World Food Programme, said in a statement.
"I also look forward to bringing my experience in governance and compliance to bear on the important reform work that is already underway at FIFA."
Bullet-proof World Cup selection
Meanwhile, this week, FIFA resumed the process to select the host of the 2026 World Cup, which had been frozen since last year over claims of misdeeds in awarding the tournaments to Russia for 2018 and Qatar for 2022.
"After all the issues, or criticisms or whatever, which happened around the last World Cup bidding process, it is absolutely crucial for FIFA's credibility that we have a bullet-poof bidding process in place for 2026," Infantino said.
He noted that human rights requirements will be examined during the process for the first time and that bidders that fail technical requirements will be excluded.
But the scandals keep haunting world football.
On Monday, Infantino's former boss, Michel Platini, said he will step down as head of European football body UEFA after failing to overturn his ban from all football-related activity over allegations that he received a dubious two million Swiss franc ($2 million, 1.8 million euros) payment from FIFA.