The film Rafiki, which means "friend" in Swahili, traces the love story between two young women.
The Kenya Film Classification Board (KFCB) said the film "seeks to legitimize lesbian romance".
KFCB warned that anyone found in possession of the film would be in breach of the law in Kenya, where gay sex is punishable by 14 years.
The film's director Wanuri Kahiu told the BBC: "I really had hoped that the classification board would classify it as an 18. Because we feel the Kenyan audience is a mature, discerning enough audience."
"I feel like the banning of the film does not allow the Kenyan audience to have a conversation about the film, and doesn't allow the Kenyan audience to even watch it and as adults decide what they think."
