Samoura, 54, spent 21 years working for the United Nations and will start at football's governing body in June.
"It is essential Fifa incorporates fresh perspectives as we continue to restore and rebuild our organisation," said Fifa president Gianni Infantino.
"She has a proven ability to build and lead teams, and improve the way organisations perform. Importantly for Fifa, she also understands that transparency and accountability are at the heart of any well-run and responsible organisation."
Samoura's appointment, announced at Fifa's congress in Mexico City, completes a new-look to an organisation which has been dogged by corruption allegations under Valcke and previous president Sepp Blatter.
Blatter, who had led Fifa since 1998, stood down last year and was later suspended from football for six years for breaching ethics guidelines.
On his appointment in February, Infantino said he would "work tirelessly to bring football back to Fifa and Fifa back to football".
Samoura, who will undergo an eligibility check before her role is ratified, currently works for the UN in Nigeria, and speaks four languages.