Smell and odours play a vital role in social interaction. Halitosis is a social problem that affects one third of the population, causing a negative impact on the quality of life. There is little knowledge on the prevalence and management of halitosis in multiple sclerosis (MS) patients. The present study aims to evaluate the presence of halitosis in patients with MS when compared to a control group, and also evaluate treatment of the problem with antimicrobial photodynamic therapy (aPDT). This is a case-control clinical study in which 60 patients were evaluated: 30 MS patients in treatment at the Specialties Clinic School of Medicine, and 30 healthy patients, matched in age and gender for the control group. Data was collected on the duration of the disease as well as the degree of disability and medication use in the MS group. For all patients, halitosis was assessed with Oral Chroma™. Individuals with halitosis underwent treatment with tongue scraping and aPDT. The photosensitizer was methylene blue (0.005%) and a THERAPY XT-EC laser (660 nm, 9 J, 100 mW for 90 s per point, 320 J cm, 3537 mW cm) was used. Six points 1 cm apart from each other were irradiated in the tongue dorsum. There was a positive correlation between the disability and disease duration. No parameter was correlated with halitosis. Patients with MS have higher levels of SH compounds when compared to the control group (p = 0.003, Mann-Whitney), but after aPDT both groups significantly reduced the levels to under the halitosis threshold. The aPDT scraping treatment was effective in the immediate reduction of halitosis in both groups.