SFO to close busiest runway for much of September: what...

San Francisco International Airport will close its busiest runway section for 20 days starting Sept. 7 for construction, reducing the number of flights by 13%.

Delays of 30 to 45 minutes on average are expected for all flights after 9 a.m., with some flights delayed up to two hours.

The 28L runway serves 68% of flights and must be repaired at a cost of $17.2 million, the airport said.

United Airlines said Monday it would allow customers to change flights from, to and connecting at SFO without paying a fee during the closure, which lasts through Sept. 26. Those who booked before Monday will pay no change fee or fare difference for flights between the same cities originally ticketed. For flights booked afterward, United may charge the difference between the old and new fares.

“We know this could be a challenging time for our customers traveling through San Francisco, and we want to provide them the flexibility they need to adjust their plans and get to their final destinations,” Matt Miller, vice president of United’s San Francisco hub, said in a statement. United accounted for 45% of airline traffic last year, the most of any airline.

Alaska Airlines, the second-largest SFO operator, didn’t respond to requests for comment. In an advisory on its website, the airline recommended signing up for flight notifications and checking flight status before leaving for the airport.

American Airlines , which operated 8% of SFO flights last year, has adjusted its flight schedule in response to the closure and notified affected travelers , said Curtis Blessing, a company spokesman. Those customers can change flights without fees or seek a full refund, he said.

Rick Seaney, CEO of FareCompare, a flight search website, suggests customers rebook flights to dates that aren’t during the closure unless they’re willing to wait out delays for a potentially better deal.

“If it’s a super cheap price and you’re going to book it, that’s totally fine if you have time on your hands,” he said. “It’s going to get backed up.”

SFO is building a new base layer of rock and cement below the runway surface. The airport repaved the top layer of the runway in 2017 and found that cracking had occurred due to heavy traffic. The federal government is funding the repairs.

Seaney said more runways are closing for repairs around the country because of aging infrastructure.

Not reconstructing the section could lead to future closures and more delays and cancellations, according to the airport.

This year, 22.2% of SFO’s departures were delayed and 27.1% of arrivals were delayed, according to the U.S. Department of Transportation. That’s higher than the national rate of 19.8% delays for arrivals and 19.2% for departures. Arrivals and departures were canceled around 2.6% of the time at SFO, compared to 2.3% nationwide.

If you’re traveling On United: Flights to or from San Francisco for travel Sep. 7-26 booked on or before Aug. 25 can be rescheduled without a change fee or extra fare. For flights booked after Aug. 25, the change fee is waived. 800-864-8331, united.com On American: Customers whose flights were rescheduled can change flights without fees or seek a full refund. 800-433-7300, aa.com On Alaska: The airline recommends signing up for flight notifications and checking flight status. 800-654-5669, alaskaair.com Editor’s note: This story has been updated to clarify which American customers can seek flight changes or refunds without the usual fees. Sources: San Francisco International Airport, Chronicle research

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SFO has two pairs of parallel runways, which can accommodate around 60 arrivals per hour, according to its website. If there is low visibility — such as from fog — aircraft must arrive single-file, which reduces arrivals to 30 per hour.

Ridership has grown at SFO, with a record number of travelers in fiscal 2017 and 2018 — though the numbers leveled off for fiscal 2019, which ended in June. The airport opened a new $2.4 billion terminal in July with nine gates. An additional nine gates will open in March.

SFO said in March that it had picked September for the closure to avoid the busier summer and holiday seasons.

During repairs, Moscone Center will host two large conventions: Oracle OpenWorld and the American Dental Association’s annual meeting.

SFO closed two runways, including 28L, last September for maintenance, leading to hundreds of canceled and delayed flights.

Officials at Oakland International Airport and San Jose International Airport said they were aware of SFO’s repair work and were prepared for flight diversions if necessary.

Roland Li is a San Francisco Chronicle staff writer. Email: roland.li@sfchronicle.com