The incident took place on Devon Close in the Woodhouse area of the city on Monday afternoon.
West Yorkshire Police today said the male youth had been charged with possession of a firearm with intent to cause fear of violence.
The youth, who was due to appear before magistrates in the city today, has also been charged in connection with a criminal damage incident on Roundhay Grove in Chapeltown on Monday.
A 15-year-old male charged in connection with both incidents was remanded into custody after appearing at Leeds Youth Court yesterday.
Shots were fired at a house on Devon Close at about 3.40pm on Monday, with a window being smashed at an address on Roundhay Grove shortly afterwards.
Detectives said yesterday that they believed the incidents were linked to a shooting on Pasture Road in Harehills on Monday evening.