Jacktone Odhiambo, a freelance photographer said to be a lover of the victim, pleaded not guilty Wednesday after being charged with murder in a court in the Rift Valley town of Eldoret.
"I did not kill him," Odhiambo said.
He will remain in custody until a bail hearing on February 16.
A post-mortem found that Chiloba, a 25-year-old model and fashion designer, had been smothered to death, with a piece of denim tied around his mouth and nose and socks stuffed into his mouth.
His body was discovered about 40 kilometers outside Eldoret after it was reportedly dumped from a moving car.
The killing was initially suspected to have been a hate crime, as members of Kenya's LGBTQ community often face harassment and physical attacks in the predominantly conservative Christian nation.
Chiloba was targeted by online abuse even after his death, which has prompted calls from rights campaigners for heightened efforts to protect members of the LGBTQ community.
Homosexuality is taboo in Kenya, as well as in much of Africa, and gay sex remains a crime with penalties including prison terms of up to 14 years.