The benefits of physical activity (PA) on health are well documented. However, inactivity among university students is prevalent. This study examined whether emotional intelligence (EI) was one of the possible underlying psychological mechanisms responsible for behavior change that may be associated with the low levels of effectiveness of PA interventions. The purposes of this study were: (1) to compare EI, health-related physical fitness (HRPF), and health-related quality of life (HRQL) for the different levels of PA in Taiwan college students; (2) to explore the predictability of PA levels, HRQL, and HRPF towards EI. A total of 599 Taiwan college students were assessed utilizing HRPF measurement, and two questionnaires including the Bar-On Emotional Quotient Inventory (EQ-I) and the Medical Outcomes Study 36-item Short-Form Health Survey (MOS SF-36). College participants who reported a recommended level of PA scored significantly higher than their insufficient and inactive counterparts in EI, and some measures of HRQL and HRPF. The variables of “physical activity”, “mental health”, “gender”, “social function”, and “flexibility” were found to be the best linear combination to significantly (p < 0.05) predict the EI of Taiwan college students. It was concluded that participation in PA might be an effective way to improve the physical, psychological, as well as emotional health of college students. Thus, the importance of increasing exercise participation at the college level should be reinforced and implemented. The findings provide a basis for research aimed at determining the causal relationship between EI and PA.