The main purpose of this study was to investigate the fitness education model implementation in a real physical education teaching setting. Specifically, this study focused on the cultivation of future exercise habits and the difficulty factors in a self-designed and self-implemented fitness program. A physical educator with seven-year teaching experience, and sixty-four college students (52 females; 12 males) enrolled in an elective “Physical Fitness” course were the participants in this study. The semester duration was 18 weeks. Students met once a week for 90 minutes. Teaching methods included teacher lectures, teaching aids, fitness testing, unit demonstrations and activities, student self-designed and self-implemented fitness program, and group or individualized discussions. The fitness test and questionnaires were administered on the second and last week of the semester. Dependent t-test, content analysis, and descriptive statistics were used to analyze the data. Findings of this study were: (1) cardio-respiratory endurance, abdominal strength and endurance, and flexibility were significantly improved after the course; (2) most students (76.6%) thought the “Physical Fitness” course was helpful to cultivate future exercise habits; (3) the self-designed fitness programs had four common difficulty factors: the control of intensity, the selection of exercise mode, awards and controls, and the arrangement of activity schedules; and (4) the self-implemented fitness programs had three common difficulty factors: laziness or too many excuses, unable to follow the activity schedule, and weather problem.