Activist Edwin Chiloba's remains were found on Tuesday near Eldoret town in Uasin Gishu county, where he ran his fashion business, independent rights group the Kenya Human Rights Commission (KHRC) said.
Motorbike taxi riders alerted police after they saw the box dumped by the roadside from a vehicle with a concealed number plate, The Standard and The Daily Nation newspapers reported, quoting police sources.
"He was brutally killed & dumped in the area by unknown assailants," KHRC said on Twitter.
"It is truly worrisome that we continue to witness escalation in violence targeting LGBTQ+ Kenyans."
Kenya National Police Service spokesperson Resila Onyango said she would comment at a later time. Uasin Gishu County Commander Ayub Gitonga Ali declined to comment.
Under a British colonial-era law, gay sex in Kenya is punishable by 14 years in prison. It is rarely enforced but discrimination is common.
"Words cannot even explain how we as a community are feeling right now. Edwin Chiloba was a fighter, fighting relentlessly to change the hearts and minds of society when it came to LGBTQ+ lives," GALCK, a Kenyan gay rights group, said on Twitter.