The boy was charged under the Air Navigation Act in relation to three incidents with planes flying in and out of Edinburgh Airport last year.
Police in Fife began investigating after it was indicated that the laser was coming from the Dalgety Bay and Rosyth areas.
Sergeant Iain Geddes said: "Following prolonged inquiry by my officers, we have now identified a 13-year-old youth as being responsible and he will be reported for this.
"I must emphasise that this is an incredibly dangerous activity and puts at considerable risk the staff and passengers of aircraft and, subsequently, the wider community should an aircraft get into difficulty.
"I would ask that those involved in this practice seriously consider their actions and for those buying and/or selling laser pens to be mindful of the uses to which they can be put."
A spokesperson for Edinburgh Airport said: "We welcome the police's determination in this matter, which underlines the seriousness of the offence. These types of offences are extremely foolhardy and could have fatal consequences.
"We hope that this action will send a message that dangerous behaviour cannot be tolerated."
Anyone with information about these alleged crimes, or anyone with other relevant information, can call Fife Police on 08456 005 702 or Crimestoppers anonymously on 0800 555 111.