A teenage boy has been charged after he and several other youths allegedly threw rocks at a moving tourist train in northern Queensland on Saturday, seriously injuring a young boy.

The five-year-old boy, visiting with his family from Japan, was aboard the Kuranda Scenic Railway on Saturday afternoon when the rock was thrown just before 4pm, near an intersection in Cairns North.

The boy was taken to Cairns Hospital with serious injuries, and flown to Townsville Hospital on Sunday.

Detective Inspector Cindy Searle said a "tennis ball-sized" rock hit the child on his forehead and he suffered a hairline fracture.

His condition is now stable, according to Townsville Hospital and Health Service.

Inspector Searle said there were "a number of youths who were throwing rocks" from around the rail line.

She said a 14-year-old boy, previously known to police, has since been arrested and charged with endangering the safety of a person in a vehicle with intent.

"We believe that there were four children involved, so we do have three other people that we are conducting investigations in relation to," she said.

"When there are a number of rocks being thrown it's difficult to ascertain exactly who has thrown which rock, so as to say whether he was the sole perpetrator."

Police are appealing for any witnesses or footage of the area from the time of the incident.

The rock was thrown near the intersection of James and Law streets, as the train neared its final destination in Cairns on its way back from the rainforest village of Kuranda.

A Queensland Rail spokeswoman said the authority had been in touch with the boy's family to check in with them following the incident.

Services on the Kuranda rail line have continued as normal.