Flu and Pneumonia Shots for Immunocompromised People

By Linda Rath | March 5, 2026   

The Centers for Disease Control and Prevention (CDC) has changed its messaging around vaccines for healthy people, but the advice for people with immune systems that don’t function correctly is the same: An annual flu shot, a pneumonia shot and, yes, a COVID shot are important for people who have autoimmune conditions like rheumatoid arthritis (RA) and lupus. These diseases and medicines used to treat them weaken the immune response, leaving patients more vulnerable to serious infections, especially respiratory infections. 

No matter how the vaccine guidelines shift, “rheumatologists are all in” on them, says rheumatologist Leonard Calabrese, DO, who heads Cleveland Clinic’s Clinical Immunology section and manages its Clinical Immunology Clinic. “We want all of our patients to get vaccinated. And we want all of their families to get vaccinated because they’re the ones who are going to give it to [our patients].” 

Flu Risks  

The 2025-2026 flu season was one of the worst in a decade. The U.S. alone saw 27 million cases, 350,000 hospitalizations and 22,000 deaths, including 101 children, by the end of March 2026, according to CDC data. (About 85% of those were unvaccinated children.) Despite a late-breaking mutation, the 2025-2026 vaccine was about 38% to 41% effective for adults, which is lower than usual, but still prevented thousands of hospitalizations and deaths, researchers say. 

Flu Vaccines for Children and New Moms 

The CDC recommends that almost everyone 6 months of age and older get vaccinated against flu by the end of October each year. The flu typically circulates between October and May. People age 65 and older should receive a high-dose or “adjuvanted” vaccine, which is stronger and longer-lasting, because their response is less robust than younger adults’ response.  

Children can get vaccinated as soon as the vaccine becomes available. Children under 9 who have never been vaccinated or who got only one shot in a previous flu season need two doses. They should get the first dose as soon as the vaccine is available, because the second needs to be given at least four weeks after the first. The first dose primes the immune system, and the second dose helps prevent infection. This two-dose approach ensures that kids are as protected as possible.  

Early flu vaccination is also possible for women in the third trimester of pregnancy; this can help protect their infants during the first months of life, when they’re too young to be vaccinated themselves. COVID vaccines are also safe and recommended for pregnant women. 

Vaccination will not always prevent the flu but it will make the infection less serious and it won't last as long.  

And don’t worry, “a flu shot will not give you the flu or increase your risk of a flare,” says Elaine Husni, director of the Arthritis & Musculoskeletal Treatment Center at Cleveland Clinic. “The non-live vaccines like the flu and pneumonia shot are very needed and necessary for patients who are immunocompromised because they are more susceptible to flu and pneumonia.”  

However, people who have a compromised immune system should avoid the nasal spray flu vaccine (FluMist). It contains a live virus that can be dangerous for people who have weakened immune systems. The virus in the vaccine shot has been inactivated and can’t cause you to get sick. 

Pneumonia Vaccine Recommendations 

It’s also important to protect yourself from pneumonia, a common but potentially fatal lung infection. It can result from flu or COVID-19, but the most common source is the pneumococcal bacterium. 

“There is an effective vaccine for that,” Dr. Calabrese says. “The pneumonia vaccine is recommended for [immunocompromised kids ages 2 to 5] and all individuals over age 19 who are immunocompromised — that means rheumatic disease patients on immunosuppressant therapies, like methotrexate, [corticosteroids], biologics and beyond.” 

Like the flu shot, it won’t necessarily prevent you from getting pneumonia, but it can reduce the severity of the disease if you do get it. 

The pneumonia shot using newer conjugate vaccines is only given once. Dr. Calabrese advises his patients to get a second dose after five years, while acknowledging that not all experts agree.    

Is It COVID or Flu? 

Because symptoms of the flu and COVID-19 are similar, knowing when to get tested for COVID-19 vs the flu can be confusing. If there’s any doubt and you have symptoms, get a COVID test, say experts. 

Flu vaccines and COVID-19 vaccines can be given at the same time. A study published in June 2026 found that receiving flu and COVID shots on the same day did not raise the risk of side effects. Some medications, including methotrexate and the biologic rituximab, can reduce the flu vaccines’ effectiveness, so most rheumatologists advise holding off on using them for a couple of weeks after vaccination.  

Even after you’re vaccinated, it’s important to continue taking measures to protect yourself — and other people — including washing your hands frequently and even wearing a mask in very crowded spaces or when infections are surging in your area.