A .38-calibre Ruger revolver and Unique .22-caliber pistol were among dozens of weapons found in the youngster's suitcase, police say.
Security officers made the discovery in the Cairns airport's holding bay about 6am on Monday when the boy and his 11-year-old brother prepared to board a flight to Weipa, where their father lives.
Federal police were alerted and Cairns detectives were called out to question the teen.
"He's refused to be interviewed so we don't know what his intentions were," Cairns Child Protection and Investigations Unit Det Sen-Sgt Glenn Horan said.
"It's unusual for someone so young to have possession of firearms at all, let alone to have such a large number of weapons."
The brothers had flown from Karratha, in northern WA, to Perth and then to Cairns.
Police also seized 14 knives, including two tactical knives and two throwing blades, more than 3000 rounds of ammunition and gun scopes.
All the weapons were allegedly stolen from a gun shop at Karratha.
An airport security source yesterday said that bags were randomly checked in holding areas at the Cairns domestic airport and they believed that was the most likely reason the weapons were found.