College students have low levels of physical activity (PA); however, PA enhancement is suggested to serve as a gateway to the improvement of other forms of health behavior. Graduate Ready for Activity Daily (GRAD) by Sallis et al. (1999) is a PA enhancement course for college students immediately before graduation. The program contains the behavior change skills needed to adopt and maintain regular PA. Moreover, there is also a need to consider PA intervention for freshmen, from the same viewpoint as GRAD. The purpose of this study was to determine whether or not a behavioral science-based physical education program with homework would have positive effects on the psychological, behavioral, and physiological variables related to the PA of college freshmen. The project was named “First-Year Physical Education” (FYPE). College freshmen from an institute of technology in the Kinki area of Japan participated in this study ( N =993; intervention group, N =497; non-intervention group, N =496). The programs that were common to all the classes were as follows (the numbers correspond to the sequence of activities in the program): (1) guidance, (2) health-related physical fitness test, (3)–(6) sports activity, (7) lecture on PA and health, (8)–(12) sports activity, (13) health-related physical fitness test, and (14) summary of the program. The PA enhancement programs were meant only for the intervention group. The programs consisted of education on behavioral change skills (decisional-balance analysis, changing self-talk, relapse prevention, social support, shaping, and so on), and out-of-class practical assignments such as active homework (self-monitoring and goal setting with regard to PA). The duration of the weekly program was 3.5 months. We measured psychological variables (self-efficacy and decisional balance [pros–cons] for exercise), behavioral variables (PA level according to the intensity and frequency of categorized PA), and physiological variables (health-related physical fitness, i.e., cardiovascular endurance, flexibility, muscular endurance, and percentage body fat). These variables were measured both before and after the class term; the intervention and the non-intervention groups were subsequently compared. Two-way ANOVA and post hoc test revealed a significant intervention effect for psychological variables such as self-efficacy and the pros of exercise. With regard to the behavioral variables, a significant intervention effect was observed for both the PA levels of “exercise and sports” and “daily activity” and the frequency of the categorized PA (daily PA, health-related exercise such as aerobic exercise, stretching, and muscular exercise). In the health-related physical fitness test with regard to physiological variables, a significant intervention effect was observed for muscular endurance. These results suggest that this behavioral science-based physical education class with homework has comprehensive positive effects on the psychological, behavioral, and physiological variables related to the PA of college freshmen.