Background: Gamification is a novel active methodology used in Physical Education to motivate students. Purpose: This study analyzed the impact of this method on the motivation of Compulsory Secondary Education students in Spain during an 8-session Physical Education Didactic Unit. Methods: A total of 275 students participated, divided into a gamified group (n = 133) and a control group (n = 142). The participants filled out 2 questionnaires, one aimed at assessing Basic Psychological Needs (BPNs) (Basic Psychological Needs in Exercise Scale) and the other at measuring the motivational component (The Sport Motivation Scale). Results: An interaction effect (Time x Treatment) was found, with the gamified group improving in BPNs (autonomy (F(1) 57.97, p = <0.001; [eta][superscript 2][subscript p] = 0.175); competence (F(1) 37.28, p = <0.001; [eta][superscript 2][subscript p] = 0.120); relatedness (F(1) 51.49, p = <0.001; [eta][superscript 2][subscript p] = 0.159), and intrinsic motivation (F(1) 39.65, p = <0.001; [eta][superscript 2][subscript p] = 0.127), while decreasing in amotivation (F(1) 21.42, p = <0.001; [eta][superscript 2][subscript p] = 0.073)). Conclusions: These data suggest that a gamified intervention enhances the satisfaction of the basic psychological needs, increases intrinsic motivation, while decreases amotivation in secondary education students.