Multiple sclerosis (MS) is a demyelinating, chronic, and progressive autoimmune disease of the central nervous system that causes the loss of axons and grey matter, and has a high prevalence in young female patients. Fingolimod is an oral treatment agent that acts by blocking the passage of the T lymphocytes responsible for the pathogenesis of MS from lymphoid tissue into the peripheral blood. We aimed to research the effects of menstrual cycles on leukocytes and lymphocyte levels in RRMS (relapsing-remitting MS) patients who received fingolimod treatment. This study was performed to determine the most suitable phase of the menstrual cycle in patients with RRMS for follow-up assessment of lymphopaenia levels after fingolimod treatment. The study population consisted of 41 RRMS patients receiving fingolimod therapy and 33 healthy women of reproductive age. Complete blood counts were performed in three different phases of the menstrual cycle, and the two groups were compared. Variability in the total leukocyte, lymphocyte, and neutrophil immune cell numbers between cycles was examined. The results indicated that total leukocyte, neutrophil, and lymphocyte levels were decreased in RRMS patients receiving fingolimod treatment, but these changes were not related to the phase of the menstrual cycle. In our study, leukocyte levels in healthy individuals were significantly lower in the proliferative phase than in other phases. The results indicated that lymphocyte monitoring in RRMS patients receiving fingolimod treatment can be performed at any stage of the menstrual cycle.