Background Multiple Sclerosis (MS) is a disease that appreciably impacts on the quality of life of patients and is associated with high expenditure. MS is a chronic multifactorial disease, characterized by inflammation, demyelination and axonal loss. The Brazilian public health system provides pharmacological treatment as well as hospital and outpatient care for patients with relapsing-remitting and secondary progressive multiple sclerosis. However, we are not aware of any previous publications assessing total direct medical costs in patients with a long follow-up within the Brazilian healthcare system. Consequently, the objective is to analyze public spending on patients with MS to guide stakeholders in future investment and disinvestment decisions. Methods and findings We retrospectively analyzed public Brazilian spending on patients with MS between 2000 and 2015 using the patient-centered registry of all patients in the public health system (SUS) obtained through deterministic-probabilistic record linkage of the Outpatient Information System, Hospital Information System and Mortality Information Systems in Brazil. Descriptive data analysis and a multiple linear regression model was performed to evaluate the associations between the mean annual cost per patient and the clinical and demographic variables. The suitability of the model was verified from a residue analysis and the level of significance adopted was 5%. Results 28,401 patients were identified and subsequently 23,082 patients were analyzed. The majority of the patients were female (73.3%), lived in the southeast region (58.9%), had a mean age of 36.8 (± 12.2) years and started treatment using one of the interferons beta (78.9%). The total direct medical cost spending in the sixteen years of the follow-up was US $ 2,308,393,465.60, and the mean annual expenditure per patient was US $ 13,544.40 (± 4,607.05). In the best fit model (p <0.001), approximately 40% of the variability of the mean annual cost per patient was explained by the region of residence; medication used (intention to treat); if the patient was a non-exclusive user of medicines, i.e., used SUS for other procedures other than high-cost medicines; year of treatment start; and presence of events (death; Relapse; change of treatment and/or comorbidity). Conclusions In the public health system of Brazil, disease modifying therapies currently represent almost all of the total direct costs of multiple sclerosis treatment. Around the world, new and emerging health technologies to treat of MS impose a challenge to health budgets, highlighting the need for cost-effectiveness studies comparing these technologies to those already available. Our regression model may help in this process, and calls attention to the need to access the real world performance of new therapies available in SUS, with the potential for disinvestment and/ or price reductions if needed.