Antibiotics and Antifungals — During Chemotherapy
Many chemotherapy regimens include antibiotics or antifungals to prevent infection before it starts, not to treat one. Knowing what each medicine is for — and why reaching for your own antibiotics at home is not a safe substitute — is part of getting through treatment safely.
Medically reviewed by Dr. N. Kiranmayee, Medical Oncologist · Last reviewed September 2026
- Prevention, not treatment — These medicines are often given to stop an infection from starting, not because one is already there.
- Not the same as home antibiotics — Spare antibiotics from a previous illness do not cover the specific infections that threaten you during chemotherapy.
- A fever is still an emergency — Being on preventive medicines does not mean a fever can be managed at home. Call your team or go to hospital.
- Your team decides which is right — The specific medicines depend on your regimen, your cancer type, and your individual risk.
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Yes, many chemotherapy regimens include preventive antibiotics and antifungals as a routine measure, not because you already have an infection. Chemotherapy lowers your white blood cell count, making infections that a healthy immune system handles easily become dangerous. NCCN guidance supports prescribing these medicines before any infection appears, based on your specific regimen and risk.
Why are antibiotics and antifungals given before any infection appears?
Chemotherapy targets fast-growing cells, which includes the white blood cells that fight infection. When those counts fall low enough, infections that a healthy immune system would handle easily can become serious within hours.
Your oncologist may prescribe preventive medicines — a practice called prophylaxis — based on how much your regimen is expected to lower your counts. Which medicines are chosen depends on your treatment and your personal risk profile.
Cotrimoxazole, sold as Septran or Bactrim, is commonly prescribed to protect against Pneumocystis pneumonia, a lung infection that is rare in healthy people but serious in someone whose immune system is suppressed. Antibacterial medicines such as ciprofloxacin (Ciplox) or levofloxacin (Levoflox) may be used during periods when counts are expected to fall very low.
Antifungals such as fluconazole (Zocon, Forcan) or itraconazole (Canditral) protect against Candida, a yeast that can spread into the bloodstream when immunity is reduced. Patients on certain regimens — particularly for blood cancers — may be prescribed posaconazole (Noxafil), which covers a broader range of fungi.
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Is it safe to take your own antibiotics if you feel unwell during chemotherapy?
No. Spare antibiotics from a previous prescription are unlikely to cover the organisms that threaten someone with low white blood cells. More dangerously, they can reduce a fever and hide exactly the warning sign your team most needs to see.
A fever during chemotherapy is a medical emergency. Call your oncology team or go to hospital rather than managing it at home — even if you are already taking preventive medicines. Preventive medicines reduce risk; they do not eliminate infection.
Tell your team about anything you have taken, including supplements and medicines bought without a prescription. They need that information before any blood tests or cultures are done.
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Frequently asked questions
Are preventive antibiotics given to everyone on chemotherapy?
Not to everyone. They are prescribed when your regimen is likely to bring your white blood cell count low enough to significantly increase infection risk, or when a specific infection risk applies to your treatment. Regimens for blood cancers and those used around bone marrow transplants commonly include prophylaxis. Many solid tumour regimens do not. Your oncologist will explain whether your treatment requires it.
What is cotrimoxazole given for during chemotherapy?
Cotrimoxazole — sold as Septran or Bactrim — protects against Pneumocystis jirovecii pneumonia, a lung infection that is uncommon in healthy people but can become life-threatening when the immune system is suppressed. It is one of the most commonly prescribed preventive antibiotics in oncology. Your team will tell you whether it applies to your regimen.
Why am I given an antifungal when I do not have a fungal infection?
For the same reason an antibiotic is given before a bacterial infection — to stop one from starting. When your white blood cell count is very low, fungi that normally live harmlessly on your skin or in your gut can enter the bloodstream and become dangerous. Fluconazole (Zocon, Forcan) and itraconazole (Canditral) are the most commonly prescribed antifungals for this purpose. Posaconazole (Noxafil) may be used for higher-risk regimens.
Can I take antibiotics from home if I feel unwell on chemotherapy?
No. Leftover antibiotics from a previous illness are not the right treatment for infection during chemotherapy, and taking them creates two serious problems. They are unlikely to cover the organisms that threaten someone with low white cells. And they can reduce a fever and mask the warning sign your team most needs to act on. A fever during chemotherapy means call your team or go to hospital — not treat at home.
What if I develop a fever while I am already on preventive antibiotics?
Call your oncology team immediately or go to your nearest emergency department. Preventive antibiotics reduce the risk of infection; they do not eliminate it. A fever on top of prophylaxis means the preventive medicine was not enough, and you need assessment, blood tests, and blood cultures without delay. Do not assume the fever will settle because you are already taking an antibiotic.
Do preventive antibiotics protect me from all infections during chemotherapy?
No. They protect against a specific set of infections your team judged you were most at risk from — not all bacteria, all fungi, or any viruses. Good hand hygiene, avoiding contact with people who are unwell, and reporting a fever promptly are still essential, even when you are on prophylaxis.
What should I tell my oncologist if I have taken medicines from home?
Tell them before any tests or blood cultures are taken — ideally at the start of your assessment. Which medicines you took, when, and for how long all matter. This will not get you into trouble; your team needs the information to make the right decisions. If you feel unwell or have a fever, go in rather than waiting to mention it at your next scheduled appointment.
When would an antibiotic be given to treat an infection rather than prevent one?
If you develop a fever or signs of active infection during chemotherapy, your team may start a treatment-level antibiotic while waiting for blood culture results to identify the cause. The medicines used for treatment are often different from the ones used for prevention, and the choice depends on the culture results, locally common organisms, and your previous antibiotic history. Your team will adjust as the picture becomes clearer.
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