In 1939, Ernie Renzel, a wholesale grocer and future mayor of San Jose, led a group negotiated an option to purchase of 483 acres (1.95 km²) of the Stockton Ranch from the Crocker family, to be the site of San Jose's airport. Renzel led the effort to pass a bond measure to pay for the land in 1940. In 1945, test pilot James Nissen leased about 16 acres of this land to build a runway, hangar, and office building for a flight school. When the city of San Jose decided to develop a municipal airport, Nissen sold his share of the aviation business and became San Jose's first airport manager. Both Renzel and Nissen were instrumental in the development of San Jose Municipal Airport over the next few decades, culminating with the opening of what is now Terminal C in 1965.

In the early 1980s San Jose International Airport was one of the first U.S airports to participate in the noise regulation program enacted by the U.S. Congress for delineation of airport noise contours and developing a pilot study of residential sound insulation. This program succeeded in its objective of demonstrating that residences in the airport vicinity could be retrofitted in a cost-effective manner to reduce interior sound levels from aircraft noise substantially.

American Airlines opened a hub at San Jose in 1988, using slots it obtained in the buyout of Air California in 1986. Reno Air, a startup based in Reno, Nevada, took over many of American's gates until it was bought out by American in 1998. American never re-established its hub; however, it is still the airport's second busiest scheduled airline after Southwest Airlines.

In 1990, San Jose International Airport greatly expanded with the opening of Terminal A. Plans at the time called for a Terminal B to be eventually built between Terminals A and C. During this peak, United Express operated regional air service to its SFO hub every thirty minutes.[citation needed]

In November 2001, the airport was renamed after Norman Yoshio Mineta, who is a native of San Jose, its former mayor and congressman, and former United States Secretary of Transportation. In December 2003, the airfield was named after former mayor Ernie Renzel.

After the dot-com bubble burst, the city lost several flights because of a decrease in demand. Air Canada discontinued its flights to Toronto and Ottawa, Canada, and American Airlines stopped its nonstop flights to Taipei, Taiwan, Vancouver, Canada and Paris, France. American also dropped its focus city service to Miami, St. Louis, Seattle, Portland, Denver, and Phoenix; the airline's flights to Southern California were downgraded to American Eagle regional flights.

Dramatic reduction at SJC continued throughout 2004. Alaska Airlines halted its San Jose - Puerto Vallarta and Cabo San Lucas seasonal routes and American Airlines discontinued its San Jose - San Luis Obispo and San Jose - Boston Logan links. In October, 2006, American Airlines discontinued the San Jose-Tokyo-Narita route, which was San Jose's last remaining link with an international overseas destination.

In April 2004, the city government, in its plan to revive the local economy, called for a restored international flight to Taipei and new international routes from San Jose to the United Kingdom, Hong Kong, China, Vietnam via Taiwan, and India.

Gate and waiting area in Terminal AIn August 2004, the city broke ground on North Concourse, the first phase in a three-phase, nine-year expansion plan. The master plan, designed by Gensler and The Steinberg Group, called for a single consolidated terminal that contains 40 gates (eight more than present), an international concourse, and expanded security areas. The terminal would be named after James Nissen. The sail-shaped facade would greet up to 17.6 million passengers a year. A people mover system would link the new terminal with VTA light rail and the planned BART station adjacent to the current Santa Clara Caltrain station. Cargo facilities would be moved to the east side of the airport. A long term parking garage would be constructed at the current location of the rental car operations. A new short term parking structure would also be constructed at the site of current Terminal C short term parking lot.

On November 16, 2005, a scaled-back airport improvement plan was approved and announced. The new two-phase plan called for a North Concourse, which is expected to be completed in 2010, and a simplified Terminal B, rather than the initially proposed James Nissen Central Terminal, to replace the aging Terminal C. In addition, Terminal A will be expanded for additional check-in counters, security checkpoints, and drop-off/pick-up curbside space. The new plan is projected to cost $1.3 billion, less than half of the original plan's cost of $3 billion.