Studying multiple sclerosis (MS) and its treatments requires the use of biomarkers for underlying pathological mechanisms. We aim to estimate the required sample size for detecting variations of biomarkers of inflammation and oxidative stress. This is a post-hoc analysis on 60 relapsing-remitting MS patients treated with Interferon-β1a and Coenzyme Q10 for 3 months in an open-label crossover design over 6 months. At baseline and at the 3 and 6-month visits, we measured markers of scavenging activity, oxidative damage, and inflammation in the peripheral blood (180 measurements). Variations of laboratory measures (treatment effect) were estimated using mixed-effect linear regression models (including age, gender, disease duration, baseline expanded disability status scale (EDSS), and the duration of Interferon-β1a treatment as covariates; creatinine was also included for uric acid analyses), and were used for sample size calculations. Hypothesizing a clinical trial aiming to detect a 70% effect in 3 months (power = 80% alpha-error = 5%), the sample size per treatment arm would be 1 for interleukin (IL)-3 and IL-5, 4 for IL-7 and IL-2R, 6 for IL-13, 14 for IL-6, 22 for IL-8, 23 for IL-4, 25 for activation-normal T cell expressed and secreted (RANTES), 26 for tumor necrosis factor (TNF)-α, 27 for IL-1β, and 29 for uric acid. Peripheral biomarkers of oxidative stress and inflammation could be used in proof-of-concept studies to quickly screen the mechanisms of action of MS treatments.