President Marius Vizer ruled that "according to the principles and spirit of judo," Wojdan Ali Seraj Abdulrahim Shahrkhani could not fight with a headscarf.
Judo officials said they were very proud their sport was one of the first to welcome a Saudi female competitor, but announced on the eve of the London Games that she would not be allowed to fight with a headscarf even though the federation has not banned women from covering their hair before.
Federation spokesman Nicolas Messner said the decision was made due to safety concerns.
"In judo we use strangleholds and chokeholds so the hijab could be dangerous," Messner said, adding that the Japanese martial art does not recognize differences in things like politics or religion.
"The only difference between competitors should be their level of judo," Messner said.
Asian judo federations have previously allowed Muslim women to wear headscarves during major competitions, but Messner said the IJF had decided against it.
The ruling Thursday could jeopardize Shahrkhani's participation in the Olympics. Saudi leaders only agreed to send women to the Games for the first time on the condition they be allowed to wear appropriate clothing for Muslim women, including a headscarf.
Shahrkhani was given a special invitation from the International Olympic Committee to compete in London. She has never fought at the international level before and has mostly been coached by her father, a judo coach and an international referee.
The 18-year-old will compete in the over 78-category at the Olympics. She was drawn to first fight Melissa Mojica, from Puerto Rico Aug. 3.
Headscarves are allowed in taekwondo. The World Taekwondo Federation changed its rules in recent years to accommodate Muslim female athletes. Some of the strongest medal contenders at the Olympics in the female division of the sport are from Egypt and Iran.
But all taekwondo fighters must also wear a headguard which is worn over a headscarf.
FIFA recently reversed it five-year ban on headscarves and now allows women to play football with their head covered.