The incident was captured by a visitor to Chiba Zoological park in the eastern part of Tokyo.
With his back turned, the child does not notice the stalking 185kg lion until it collides with the glass.
The glass display was introduced in April to allow visiters a closer look at the large predator.
Animal rights campaigners have said the video highlights why keeping wild predators in such captivity is both cruel and dangerous.
Lion expert Adam M. Roberts from Born Free USA told The Dodo: "Lions are natural wild predators and the child in this video, especially when turning his back to the massive feline, becomes prey in the animal's eyes.
"The firm glass wall held the lion inside his enclosure, surely frustrating his innate instincts.
"But luckily for the family, if the barrier had not held the consequences could have been catastrophic."
Zookeepers have insisted, however, the lion only wanted to play with boy and always reacts this way whenever it sees young children.
The Independent has contacted the zoo for comment.
Join our commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies