Members of the LGBTQ community protested over Education CS George Magoha's remarks he made in December.
CS Magoha said gay learners should be restricted to day schools closer to their homes so that they don't influence other students in school.
The community on Thursday took to the streets of Nairobi, condemning Magoha's directive.
Marylize Buibwa, the convener of the procession, said that the CS is already seen as a threat towards LGBTQ kids and the broader queer community. They questioned his ability to hold his current position.
"Education must be accessible to every child of a country despite any title attached to them," she said.
Buibwa said that primary and high school students have little to no idea of what sexuality is and are still learning to understand their emotions.
"How will they understand their growth and development when the one supposed to guide them bans and excludes them from learning?" she posed.
The activists said that the ban perpetuates the marginalisation of the LGBTQ community, who would be pushed to the outskirts of the society where poverty, crime and inequality lies.
Media personality and LGBTQ activist Makena Njeri said it is not easy being a queer in Kenyan schools.
"Personally, as a person who went through the Kenyan Education system, as a queer child, I know the pressure that they go through, and I know that this directive by the CS will greatly harm them," Njeri said.
She said she was expelled several times from different schools because she identified as a lesbian.
The queer community issued demands to the Ministry of Education to curb violence and discrimination towards queer kids.
"Magoha should attend LGBTQ affirming training that would be conducted by LGBTQ organisations and groups," they said.
The training, they said, will broaden his knowledge of the LGBTQ community and their experiences and lives.
They also demanded that directives be issued to ensure queer kids, whether by coming out or by assumption, are safe and protected in learning institutions.
-Edited by B. Marita