Physical education emphasizes learning sports skills, which is why it is usually conducted in a face-to-face manner. Instructors focus on explaining rules and demonstrating moves, which the learners are required to repeat and imitate. Flipped classrooms have become a trend; thus, the present study investigated their influence on physical education. A mobile application for novice and advanced basketball players was developed and tested in a course teaching 3-on-3 basketball and various teaching methods were implemented to test for the effects of gender differences on learning outcome. The participants were students enrolled in the aforementioned course in a university in central Taiwan. 326 participants were included in the study, of whom 238 were male and 88 were female. The duration of the experiment was 5 weeks between May and June 2017, during which the correctness of moves, maneuverability, teamwork, sense of balance, and adaptability of the participants were evaluated and graded as their learning outcome. The research team observed the participants each week to gather empirical data for analysis. The results indicate that a mobile flipped classroom is the optimal teaching strategy, followed by projecting teaching; therefore, a mobile flipped classroom is the recommended approach to be integrated into physical education.