Carlos Cunningham is charged with conspiracy to distribute marijuana for his role in an alleged drug ring after agents discovered the tunnel on Tuesday.
The tunnel connects an Otay Mesa office complex and warehouse to another warehouse in Tijuana. It had lighting, ventilation and a rail system for sending carts of drugs into the United States.
The tunnel ended close to California's Otay Mesa port of entry, according to U.S. Immigration and Customs Enforcement spokeswoman Lauren Mack.
Federal agents found it after getting a tip that there was one somewhere on Via De La Amistad. On Tuesday, they spotted a suspicious looking tractor-trailer parked outside an office building.
"We ultimately decided it wasn't acting right," said San Diego I.C.E. director John Morton.
Agents followed the tractor-trailer when it left the building and headed north on I-15. When it reached the border checkpoint near Temecula, agents searched it and found 10 tons of marijuana.
Cunningham was arrested. His wife is also charged with conspiracy.
Agents obtained a search warrant at the office building on Via De La Amistad and found the tunnel along with 15 tons of pot. Four more tons were found on the Tijuana side.
Officials have found 125 tunnels since they started recording them in the early 1990s. Of those, 75 have been found in the past four years, most along the California and Arizona border with Mexico.