Referee Martin Wekesa said he was seeking $240,000 in compensation from FKF after the alleged assault in a game in September last year, when he was kicked and hit by members of the Sparki Youth team before being "attacked in my private parts" by one of the coaching staff.
Wekesa said Daudi Kajembe came onto the field and assaulted him after a decision to send a Sparki player off.
"He pulled my testicles. He actually pressed them and I was hanging on him when he was pulling me. I was crying and could not get myself out from his hands," Wekesa said. "I remember Kajembe told me, raising his hand, 'I can kill you in a minute,' and came directly to my testicles."
Wekesa was rescued by a police officer, he said, but slumped to his knees in pain on the pitch before being taken to the hospital. He is now unable to have sex with his wife, he claims, saying it is "impossible."
"It is so painful, painful, painful in my areas," he said.
Kajembe is due to appear in court in Kenya's coastal city of Mombasa on Thursday on a charge of assault and causing grievous bodily harm, while Wekesa is claiming the 20 million Kenyan shillings in compensation from the federation for his expensive medical bills and the problems the assault has caused him and his wife, Mary.
"We used to live as wife and husband. Nowadays we don't, so that's how the life has changed," Mary Wekesa said.
The referee said he had sent a letter to the Kenyan federation to demand the compensation, but had not yet heard back.
Kajembe pleaded not guilty to causing grievous bodily harm.