The boy was with two other minors and one adult, U.S. Customs and Border Protection said, when he approached the State Route 94 checkpoint in Jamul, east of San Diego, Monday night.
As border agents questioned the group, who were in a 2006 Volkswagen Jetta, a drug-sniffing K-9 alerted the agent.
The group was moved to another area for a secondary inspection. They were searched and the packages of drugs were found on the teen's waistline, a news release said.
Another 49 plastic-wrapped packages were found in three backpacks inside the car. In total, agents discovered 54 pounds of drugs worth an estimated $102,000.
Authorities arrested the 14-year-old and a 16-year-old, both Mexican nationals. The driver, a 34-year-old man, and another 16-year-old, both American citizens, were also taken into custody.
Agents in the San Diego sector have seized 42 million worth of methamphetamine since Oct. 1.