<b><i>Background:</i></b> There is a lack of head-to-head studies comparing the efficacy of fingolimod (FIN) and natalizumab (NTZ) as second-line therapy for relapsing-remitting multiple sclerosis (RRMS). <b><i>Methods:</i></b> Multicenter, observational study, in which, information of 388 patients randomly selected and treated with FIN or NTZ in routine clinical practice was retrospectively collected with the main objective of comparing the annualized relapse rate (ARR) over the first year, after FIN or NTZ treatment initiation. <b><i>Results:</i></b> Mean ARR during the first year of treatment was 0.28 in FIN group and 0.12 in NTZ group (<i>p</i> = 0.0064); nevertheless, the difference between groups lost statistical significance when the propensity score analysis was performed. Time to disability ­progression was similar in both treatment groups (12.3 ± 6.7 months in FIN, and 12.8 ± 0.1 months in NTZ; <i>p</i> = 0.4654). Treatment persistence after the first year of treatment was higher in patients treated with FIN (95%) than in those treated with NTZ (84%; <i>p</i> = 0.0014). <b><i>Conclusions:</i></b> After 12 months of treatment, both FIN and NTZ reduced the ARR, but ARR percent reduction was significantly higher with NTZ. Treatment persistence was higher in patients receiving FIN.