Kenya did not qualify for the competition but were included after the Confederation of African Football last month suspended Equatorial Guinea for fielding an ineligible player during qualifying matches in June.
The decision was overturned on appeal Wednesday.
“We are profoundly astonished by the Appeal Board of the Confederation of African Football (CAF) decision to reinstate Equatorial Guinea women’s football team to the 2018 Africa women Cup of Nations, only ten days before the start of the tournament,” said Barry Otieno, a spokesman for the FKF on Thursday.
“We feel the decision is not only a great injustice to the Kenyan women’s football team, the Harambee Starlets, but to millions of Kenyans, the Kenyan government and the national federation, which has since dedicated enormous resources in preparation for the 2018 AWCON.”
The competition will be played in Ghana from November 17 to December 1.