Fatma Samoura, 54, comes from outside the football world, having worked with the United Nations for 21 years. She is currently based in Nigeria for the UN Development Program.
FIFA president Gianni Infantino, who announced her appointment during the annual congress in Mexico City, said his future number two was "a great person" with experience managing big organizations, budgets and staff.
"We have to be serious when we say we embrace diversity and we believe in gender equality," Infantino said.
Samoura 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 honored to take on the role of FIFA's secretary general," Samoura, who has also worked at the World Food Program, 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."
Germany's Markus Kattner had been serving as interim secretary general since then.
FIFA officials gathered in the Mexican capital to formally implement changes that were adopted at an extraordinary congress in February to overcome a deep corruption crisis.
"Today we pass from the words to the actions, from the proclamations to the facts," said Infantino, who was elected in February after his predecessor Sepp Blatter was brought down by the scandal.
In another step towards restoring trust, the North and Central American and Caribbean football confederation (CONCACAF), which has been in the eye of the corruption storm, elected a new president on Thursday.
Canadian football chief Victor Montagliani became CONCACAF's fourth president in five years after his three predecessors were ensnared in corruption allegations, with the last one arrested in December.
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