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International Scheduled Flights
| Origin | Destination | Carier |
| SJD | SAN San Diego, California US | Aeromexico |
| SJD | YVR Vancouver BC, Canada CA | Air Canada |
| SJD | YYZ Toronto, Canada CA | Air Canada |
| SJD | LAX Los Angeles, California US | Alaska Airlines, Inc. |
| SJD | PDX Portland, Oregon US | Alaska Airlines, Inc. |
| SJD | SAN San Diego, California US | Alaska Airlines, Inc. |
| SJD | SEA Seattle, Washington US | Alaska Airlines, Inc. |
| SJD | SFO San Francisco, California US | Alaska Airlines, Inc. |
| SJD | OAK Oakland, California US | America West Airlines, Inc. |
| SJD | PHX Phoenix, Arizona US | America West Airlines, Inc. |
| SJD | TUS Tucson, Arizona US | America West Airlines, Inc. |
| SJD | ABI Abilene, Texas US | American Airlines, Inc. |
| SJD | AUS Austin, Texas US | American Airlines, Inc. |
| SJD | DFW Dallas / Ft Worth, Texas US | American Airlines, Inc. |
| SJD | JFK New York City, New York US | American Airlines, Inc. |
| SJD | LAX Los Angeles, California US | American Airlines, Inc. |
| SJD | ORD Chicago, Illinois US | American Airlines, Inc. |
| SJD | STL St Louis, Missouri US | American Airlines, Inc. |
| SJD | LAS Las Vegas, Nevada US | Compania Mexicana De Aviaci |
| SJD | LAX Los Angeles, California US | Compania Mexicana De Aviaci |
| SJD | SMF Sacramento, California US | Compania Mexicana De Aviaci |
| SJD | EWR Newark, New Jersey US | Continental Air Lines, Inc. |
| SJD | IAH Houston, Texas US | Continental Air Lines, Inc. |
| SJD | ATL Atlanta, Georgia US | Delta Air Lines, Inc. |
| SJD | CVG Cincinnati, Kentucky US | Delta Air Lines, Inc. |
| SJD | JFK New York City, New York US | Delta Air Lines, Inc. |
| SJD | SLC Salt Lake City, Utah US | Delta Air Lines, Inc. |
| SJD | BRO Brownsville, Texas US | ExpressJet |
| SJD | IAH Houston, Texas US | ExpressJet |
| SJD | DEN Denver, Colorado US | Frontier Airlines |
| SJD | LAX Los Angeles, California US | Frontier Airlines |
| SJD | MCI Kansas City, Missouri US | Frontier Airlines |
| SJD | SJC San Jose, California US | Frontier Airlines |
| SJD | SMF Sacramento, California US | Frontier Airlines |
| SJD | LAS Las Vegas, Nevada US | Mesa Airlines, Inc. |
| SJD | PHX Phoenix, Arizona US | Mesa Airlines, Inc. |
| SJD | SAN San Diego, California US | Mesa Airlines, Inc. |
| SJD | DTW Detroit, Michigan US | Northwest Airlines, Inc. |
| SJD | MSP St. Paul, Minnesota US | Northwest Airlines, Inc. |
| SJD | MSP St. Paul, Minnesota US | Sun Country Airlines |
| SJD | DEN Denver, Colorado US | United Air Lines, Inc. |
| SJD | ORD Chicago, Illinois US | United Air Lines, Inc. |
| SJD | SFO San Francisco, California US | United Air Lines, Inc. |
| SJD | STL St Louis, Missouri US | United Air Lines, Inc. |
| SJD | LAS Las Vegas, NV US | US Airways |
| SJD | PHX Phoenix, AZ US | US Airways |
| SJD | SAN San Diego, CA US | US Airways |
| SJD | DTW Detroit, Michigan US | USA 3000 Airlines |
International Charter Flights
| Origin | Destination | Carier |
| SJD | DFW Dallas / Ft Worth, Texas US | American Trans Air, Inc. |
| SJD | LAX Los Angeles, California US | Ameristar Air Cargo |
| SJD | YUM Yuma, Arizona US | Ameristar Air Cargo |
| SJD | MEM Memphis, Tennessee US | Boston-Maine Airways |
| SJD | DFW Dallas / Ft Worth, Texas US | Champion Air |
| SJD | STL St Louis, Missouri US | Champion Air |
| SJD | ORD Chicago, Illinois US | Ryan International Airlines |
There is over 55 international flights from SJD airport.
