Jacktone Odhiambo, a freelance photographer said to be a lover of the victim, appeared in court in the Rift Valley town of Eldoret along with four other suspects, who were freed after police said they were not linked to the killing.
"Following our investigation we have established that four of the suspects are not linked to the murder. However, the first suspect, Jacktone Odhiambo, will be charged with murder," state counsel Anthony Fedha told the court, the Daily Nation newspaper reported.
The chief government pathologist Johansen Oduor said earlier this month that Chiloba, a 25-year-old model and fashion designer, had been smothered to death.
He said after a post-mortem that a piece of denim had been tied around Chiloba's mouth and nose and that socks had also been stuffed into his mouth.
His body was discovered about 40 kilometres (25 miles) 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 have faced 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 and across much of Africa.
Despite attempts to overturn British colonial-era laws banning homosexuality in Kenya, gay sex remains a crime with penalties including prison terms of up to 14 years.
