The purpose of this study was to investigate the effects of a physical education program based on behavioral science, which includes homework (project First-Year Physical Education: FYPE) on the health level and lifestyle of first-year college students. The study participants comprised 1,090 male college freshmen from an institute of technology in the Kinki area of Japan (intervention group, N =515; non-intervention group, N =575). The programs that were common to all the classes were as follows (the numbers correspond to the sequence of activities of the program). 1: guidance, 2–4: sports activity, 5: lecture (health science), 6–8: sports activity, 9: lecture (health science), 10–12: sports activity, and 13: summary of the class. Health behavior promotion programs were intended only for the intervention group. The programs comprised (1) education on behavioral change skills (self-monitoring, goal setting, self-reinforcement, and so on), and (2) out-of-class practical assignments such as physical education homework. We evaluated the health level and life habits of the students by using the Diagnostic Inventory of Health and Life Habit (DIHAL; Tokunaga, 2003) and evaluated their physical activity level using the Physical Activity Assessment Scale (PAAS; Wakui & Suzuki, 1997). As a result, significant intervention effects were observed with regard to the DIHAL scales for “Eating,” “Resting,” and the “Sum of lifestyle,” and with regard to the subscales of “Level of physical health,” “Eating regularly,” “Relaxing,” “Sleeping regularly,” and the “Fulfillment level of sleep.” The PAAS revealed a significant intervention effect with regard to “Daily activity,” which indicates the relatively light physical activities in daily life; however, this was not observed with regard to the DIHAL scale of “Exercise.” These results clearly indicate that physical education programs based on behavioral science and including homework can improve the overall lifestyle (namely, physical activity, eating, and resting) of first-year college students.