Active methodologies have emerged in which they focus their importance of the teaching-learning process in students and not only on the result. In this way, research has been conducted using the active methodology Flipped Learning (FL) in all areas of Primary, Secondary and Higher Education. Objective: The current study aims to analyze the effect on student motivation after an intervention with the FL teaching technique, using a Parkour Didactic Unit in primary school students. Methods: One hundred students of 6th grade of Primary (11-12 years old) participated in this study, of which, 45 were girls and 55 were boys. It was randomly decided that 6ºB and 6ºD would follow the teaching styles that were already used in the center regularly (TRAD group) and otherwise, the 6ºA and 6ºC groups used FL teaching technique by watching videos created by the principal investigator for the present investigation (FLIP group). The Motivation Questionnaire in Physical Education in primary education and personal interview were applied before and after intervention. Results: The results showed an increase of intrinsic motivation (p < .001), identified motivation (p < .001) and introjected motivation (p < .001) in FLIP group. Moreover, external motivation, as well as the amotivation of the students, has decreased after the intervention. Regarding the TRAD group, a significant decrease in intrinsic motivation and identified motivation was observed. According to qualitative results, the most remarkable thing is that students consider FL as more fun, efficient, accepted and motivating. Conclusions: Intrinsic motivation increased significantly and amotivation values decrease in FL group. FL approach allows using more time in Physical Education classes and, consequently, it is perceived as more fun for the students.