Judge John Mativo said the introduction of new club licensing regulations without the participation of members and stakeholders was illegal and in violation of FIFA and CAF guidelines.
He was ruling on a petition brought by former FKF boss Sam Nyamweya.
The judge also declared that the Premier League should revert to a 16-team championship from the current 18-team format.
Immediately after the ruling two teams that had been promoted this year were suspended by the premier league’s independent organising body.
The new rules, some of which were yet to be implemented, could have seen some Kenyan clubs denied licences to take part in either the Kenya Premier League (KPL) or the second division league, or get demoted to lower leagues.
To be granted a licence by the FKF, clubs are required to adhere to certain requirements, including having an operating office, club house, pitch and proof of sufficient finances for the season.
“Such unilateral actions will bring chaos and disunity to Kenyan football and degrade the extensive strides that have been accomplished, and may cause a total ban on Kenya football by FIFA,” Mativo said in his ruling.
FKF will appeal the decision, saying: “The federation remains committed to its footballing mission and will not be distracted by the ongoing effort by a section of disgraced former football administrators, keen on suffocating the development of the game at all levels.”