Children testified that Salim Mohamed Wabwire taught them that Christians should be killed.
Contrary to earlier reports, the court in Mombasa city acquitted him of being a member of militant Islamist group al-Shabab, and recruiting for it.
The group, which is linked to al-Qaeda, has increasingly targeted Kenya.
It killed 148 people in an assault on Garissa University College in north-eastern Kenya in April.
Wabwire was a primary school teacher, and an Imam at the Jihad Mosque in a rural area north of Mombasa.
A convert from Christianity, he was previously known as Samuel Wanjala Wabwire.
While some of the children testified against him, one tried to cover up for him, the court said.