Background: Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system with varied clinical features. Disease-modifying drugs (DMDs) of MS associated with different types of thyroiditis. In this cross-sectional study, we aimed to assess the prevalence of thyroid dysfunction in MS and to investigate the association between DMDs and the risk of thyroiditis in MS. A cross-sectional study included 100 patients with relapsing-remitting multiple sclerosis (RRMS) in relapse, and the diagnosed was according to revised McDonald’s criteria 2010. Results: Our results revealed that the prevalence of thyroiditis was 40%; autoimmune (34%) and infective (6%) among patients with RRMS in relapse and cerebellar symptoms were significantly higher in patients with thyroiditis compared to patients without thyroiditis. Regarding the association between DMDs and thyroiditis, the prevalence of patients treated with interferon-beta-1b was higher in MS patients with thyroiditis compared to MS patients without thyroiditis. However, the prevalence of patients treated with interferon-beta-1a was lower in MS patients with thyroiditis compared to MS patients without thyroiditis. In addition, we found CMV infection was more common in patients treated by interferon beta-1b and candida infection was common in patients treated by fingolimod. Conclusions: Thyroiditis is commonly observed in patients with RRMS in relapse and higher prevalence of patients treated with interferon-beta-1b which is commonly associated with thyroiditis and CMV infection; however, candida thyroid infection was common in MS patients treated by fingolimod.