The purpose of this study was to analyze the effect of preferred physical activity on emotion, stress and happiness in university students. The participants of this study consisted of 23 university students and the measures were the profile of mood state (POMS), the stress scale and the happiness inventory. Participants in this study were randomly assigned to the preferred physical activity group (n=12) and the non-preferred physical activity group (n=11). Participants in the study were physically active twice a week for 60 minutes per session. The collected data were analyzed through the SPSS 23 version, and p-value<.05 was set. The results of this study were as follows. First, the group participating in the preferred physical activity significantly decreased total mood disturbance (TMD). Second, participation in the preferred physical activity significantly reduced the participants' stress symptoms. Third, there was a significant increase in happiness in the preferred physical activity group. However, there were no significant changes in TMD, stress and feelings of happiness in the non-favored physical activity group.