Background: Motivation can be considered a critical factor in encouraging and maintaining physical activity. Despite the many health benefits offered by physical activity, a significant percentage of university students do not meet recommendations. University years are a critical time for promoting and maintaining an active lifestyle. This study aimed to analyze motivations for engaging in physical activity among university students and their relationship with gender, amount of sports activity, and satisfaction with sports activity. Methods: The sample consisted of 1099 Vizcaya university students (45.3% men and 54.7% women), aged between 18 and 29 years old (M = 20.4; SD = 1.7 years). Sports motivation, the number of weekly hours of physical activity, and the level of satisfaction with sports were analyzed. (3) Results: Significant differences were found in intrinsic (d = 0.36, p = 0.000) and external regulation (d = 0.19, p = 0.002), men having a higher motivation level compared to women in these dimensions, but not in participants’ level of satisfaction. The effect of gender on the amount of physical activity was mainly direct, but motivation was significantly mediating. In addition, there was not a significant effect of gender on level of satisfaction, but analyzing its limited effect in the sample, the mediation of intrinsic regulation was significant. (4) Conclusions: To understand the variance of the amount of physical activity and satisfaction in university students, the direct effect of gender must be considered as well as the mediating role of some dimensions of motivation.