Multiple sclerosis (MS) patients frequently develop some form of ocular motor dysfunction during the disease. In previous studies, ocular motor abnormalities were found to correlate with clinical disability and with impaired cognitive performance. The objective of this study was to assess the pursuit ocular movement (POM) frequency in relapsing-remitting (RR) and secondary progressive (SP) MS patients by using a vision-based non-intrusive eye tracker. POM frequency was significantly lower (p < 0.001) in MS patients compared to normal controls. No differences between RR and SP-MS patients and no correlation between POM and expanded disability status scale (EDSS) score were found. This exploratory study suggests that our vision-based system is a new simple non-intrusive method showing impairment of POM values in MS patients, even in the absence of association with clinical disability (EDSS). Future works on larger cohorts of MS patients might validate this eye tracking in MS clinical practice.