Bactroban Side Effects: What to Expect and When to Call Your Doctor

Bactroban (mupirocin) is one of the safest prescription antibiotics available — in part because it's applied topically rather than taken by mouth, which means very little of it enters your bloodstream. Most people complete a full course without experiencing any notable side effects.

That said, side effects are possible. This guide covers what to expect, what's normal, what's uncommon but important, and the rare but serious reactions that warrant a call to your doctor.

Common Side Effects of Bactroban (Mupirocin)

The most common side effects of topical mupirocin occur at the application site. In clinical trials, these were reported in fewer than 2% of patients:

Burning, stinging, or pain at the application site (reported in 1.5% of patients in clinical trials)

Itching (reported in about 1% of patients)

Headache and rash (reported in about 1.1–1.7% of patients using the cream formulation)

Mild nausea (reported in about 1.1% of patients using the cream)

These effects are generally mild and temporary. They usually go away on their own and don't require stopping the medication. However, if the burning or irritation is severe or worsening, check in with your healthcare provider.

Side Effects of Bactroban Nasal Ointment

If you're using Bactroban Nasal for MRSA decolonization, the side effect profile is slightly different because the medication is applied inside the nose:

Headache

Runny nose or nasal congestion

Sore throat

Dry or irritated nasal passages

Altered taste (dysgeusia)

Cough

Serious Side Effects: When to Call Your Doctor Right Away

While rare, some side effects of Bactroban are serious. Contact your doctor or seek emergency care if you experience:

Severe allergic reaction (anaphylaxis): Symptoms include swelling of the face, lips, tongue, or throat; hives; wheezing; difficulty breathing; or dizziness. This is rare but a medical emergency — call 911 or go to the ER immediately.

Severe skin reaction: If the treated area becomes intensely red, swollen, or develops new blistering or peeling, stop using Bactroban and contact your provider. This may indicate a contact allergy to mupirocin or the PEG ointment base.

Antibiotic-associated diarrhea: Although very rare with topical antibiotics, Clostridioides difficile-associated diarrhea (CDAD) has been reported with mupirocin use. If you develop severe or persistent diarrhea — especially watery or bloody stools — during or up to 2 months after using mupirocin, contact your doctor immediately.

Worsening infection: If your skin infection is not improving after 3–5 days of treatment or appears to be spreading, call your provider. Prolonged use can sometimes lead to overgrowth of non-susceptible bacteria or fungi.

Special Safety Notes

Avoid eyes and mucous membranes: Bactroban ointment is not formulated for use in the eyes or nose — use the separate nasal formulation for nasal application. If you get it in your eyes, rinse immediately with water.

Don't use on extensive burns: The polyethylene glycol (PEG) in Bactroban ointment can be absorbed into the bloodstream through large open wounds, potentially causing kidney problems in people with renal impairment.

Do not use with other topicals: The prescribing information recommends not applying Bactroban ointment at the same time as other lotions, creams, or ointments, as mixing may affect how it works.

The Bottom Line on Bactroban Safety

Bactroban is among the best-tolerated topical antibiotics available. Most side effects are mild local reactions at the application site. Serious reactions are rare but real — knowing the warning signs is the most important safety step. For general information about how Bactroban is used and what it treats, see our guide: What Is Bactroban? Uses, Dosage, and What You Need to Know.