The Pentagon’s priciest new weapons program just got more expensive.

The expected lifespan for the F-35 combat jet program, already projected to cost about $1 trillion to buy and maintain more than 2,400 planes, has been extended, which will add to the overall cost.

The F-35 combat jet is expected to be the mainstay of the U.S. air power for six decades, but the Air Force plans to fly it less than previously planned, a move that would extend the life of each plane by as much as six years and add to maintenance costs.

The surprise extension to the jet’s projected life comes even before it has entered service with the Air Force, which is scheduled for later this year.

While the cost of building each jet has been falling, flying it longer will increase the estimated lifetime cost of the F-35 program for U.S. taxpayers to $1.13 trillion from $1.02 trillion a year ago, according to data released by the Pentagon on Tuesday.

The Air Force now expects to fly each jet an average of 250 hours a year compared with its earlier projection of 300. Lt. Gen Chris Bogdan, the military head of the F-35 program, said the move reflected changes to how much each plane is used for training rather than any shift in its role.

Still, the Pentagon is seeking ways to reduce the program’s costs. More than half of the costs are for operating and maintaining the fleet, and the military is working with the plane’s builders to cut those expenses.

Jet builder Lockheed Martin Corp. LMT, -0.20% and its partners have invested $170 million over two years to cut the cost of building the F-35.

An expanded version of this report is available at WSJ.com.