Interferon-beta is one of the most widely prescribed disease-modifying therapies for multiple sclerosis patients. However, this treatment is only partially effective, and a significant proportion of patients do not respond to this drug. This paper proposes an alternative fuzzy logic system based on the opinion of a neurology expert to classify relapsing-remitting multiple sclerosis patients: high, medium, and low responder to interferon-beta. Also, a pipeline prediction model trained with biomarkers associated to interferon-beta response is proposed for predicting whether patients are potential candidates to be treated with this drug, in order to avoid ineffective therapies. The classification results shows that the fuzzy system presents a 100% efficiency compared with an unsupervised hierarchical clustering method (52%). So, the performance of the prediction model is evaluated, and a 0.8 testing accuracy is achieved. Hence, a pipeline model including data standardization, data compression, and a learning algorithm, can be a useful tool for getting reliable predictions about the response to interferon-beta.