The sophisticated tunnel, lined with concrete and equipped with ventilation and lights, has apparently been used by drug traffickers, with two tonnes of marijuana found inside.
US officials discovered the tunnel, which runs from Tijuana, Mexico, to Otay Mesa, California, on Wednesday.
The tunnel is the 16th to be found in the region since September 11, 2001, according to US officials.
It was discovered by US Border Patrol agents who tipped off Mexican authorities.
The tunnel, discovered by US Border Patrol agents who tipped off Mexican authorities, begins beneath a warehouse in the Mexican border town of Tijuana and stretches to Otay, near the US border hub of San Diego.
"Mexican law enforcement officers ran through the tunnel into the United States and ultimately popped up into a warehouse in the United States," said Michael Unzueta, special agent in charge for ICE investigations in San Diego.
Beneath the warehouse, the police found a 1.8 metre by 3.6 metre shaft fitted out with electricity and a ventilation system, along with more than two tonnes of marijuana, stacked in about 60 bales.
Officials said illegal immigrants and even weapons may have also travelled through the tunnel.
The US-Mexican border stretches from San Diego on the West coast to the Gulf of Mexico across four states, is notoriously porous.