Flu Season Has Arrived in the Bay Area Early This Year — Time to Get Your Flu Shot

As the Bay Area’s summer COVID-19 wave finally tapers down, flu season is here to take its place — and it’s early this year.

According to data from Stanford University’s WastewaterSCAN project, which monitors viral levels in human sewage, seasonal onset for flu didn’t arrive until November 2025. But this year, the Bay Area has already officially hit the threshold.

Doctors generally recommend that you get your flu vaccine sometime in October, so your body has maximum immunity as the flu starts rising. But this year, the early arrival of flu season — and the Bay Area’s first death from flu in San Francisco — has several counties urging residents to get their shot sooner.

Here’s what to know about the Bay Area’s early 2026 flu season and when you should be getting vaccinated.

WastewaterSCAN’s Amanda Bidwell said that this past September, the team detected the presence of influenza in over 90% of samples from the Bay Area wastewater sites they monitored that month. Concentrations of flu in local human sewage were up almost 350% from August to September, Bidwell said.

UCSF’s lab is also diagnosing flu in its patients up to five times as much as it was a month ago, said Dr. Peter Chin-Hong, an infectious disease expert at UCSF, in an email to KQED.

On Oct. 1, the San Francisco Department of Public Health announced the city’s first death from flu in a resident. Last winter, San Francisco didn’t see any flu deaths until January.

The early arrival of flu in California “also tracks with the earlier flu activity seen in the UK, Japan, and other countries in the Northern Hemisphere,” Chin-Hong said. But this doesn’t necessarily mean that the flu season will be worse this year, he said.

The flu shot is updated every year for maximum efficacy against prevalent strains — and “We have well matched vaccines this year,” Chin-Hong said.

The general consensus is: yes. “I will probably get my flu shot on the soonish side,” Chin-Hong said. “Definitely before Halloween, and probably not wait until November.”

Marin County’s former public health officer Matt Willis, now at Your Local Epidemiologist California, wrote in his newsletter that “Now is the time to get your flu shot, if you haven’t already,” since maximum protection from the vaccine takes around two weeks to build.

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San Francisco health officials have been urging residents to seek out their flu vaccine since the agency announced the city’s first death from the disease. In a Thursday public advisory, the Santa Clara Public Health Department told residents that “Early flu activity means now is the time to protect your family against fall viruses” — including COVID-19.

The new, updated 2026-27 COVID-19 shots are also now available, and it’s completely safe to get your flu vaccine and your COVID-19 vaccine at the same time for convenience.

“Additionally, the public should be aware and cautious of rapidly spreading misinformation that questions the safety and efficacy of widely tested vaccinations that have protected us for years,” a Santa Clara County spokesperson said. “It’s important to get vaccine information from trusted messengers and qualified healthcare professionals, such as your local public health department.”

As anyone who’s had the flu can attest, the virus is no joke. The Centers for Disease Control and Prevention estimated that last flu season, there were at least 32 million illnesses nationwide, 390,000 hospitalizations, and 24,000 deaths from the flu. 

The flu vaccine reduces your risk of severe illness and hospitalization. The virus can be especially dangerous for kids, and the CDC said that a 2022 study showed flu vaccination reduced children’s risk of severe, life-threatening influenza by 75%.

If you have health insurance, a flu shot is covered and available without extra cost, as a preventive service from your usual health care provider. It’s also available at most pharmacies (see below).

You can get your flu shot at the same time as your COVID-19 vaccine — it’s completely safe to do so, and many people do.

• CDC’s Find Flu Vaccines tool
• Kaiser Permanente flu shots (Northern California)
• CVS flu shots
• Walgreens flu shots
• Rite Aid flu shots
• Costco Pharmacy flu shots
• Albertsons (Safeway) flu shots

You can get the vaccine free of charge from several Bay Area providers and community clinics if you don’t have insurance. (You can also technically use these free services even if you do have insurance, but you may consider choosing to reserve these particular resources for those without coverage).

Your county’s public health department may also be offering flu shots.

• San Francisco Department of Public Health’s AITC clinic (offers a pay-what-you-can option)
•  Contra Costa Public Health Immunization Clinic (flu shots are $15 for adults over 19, but fees may be waived if you’re unable to pay)
• Alameda County Immunization Clinics