This study aimed to analyse the effects of a parkour-based Adventure Education (AE) program on the intrinsic motivation of primary school students, and to examine the role of enjoyment, self-confidence, and resilience as associated and predictive variables, considering differences according to time (pre-test–post-test) and gender. The sample consisted of 492 fifth- and sixth-grade primary education students (249 boys and 243 girls) with a mean age of 10.67 years, enrolled in 12 Spanish schools. A quasi-experimental design with pre-test and post-test measures was used following the implementation of a seven-session program based on the Pedagogical Model of Adventure Education. Data were collected using instruments validated in the Spanish population: the Intrinsic Motivation subscale of the Perceived Locus of Causality Scale, the Physical Activity Enjoyment Scale to measure enjoyment, the Self-Confidence subscale of the Competitive State Anxiety Inventory, and the Connor–Davidson Resilience Scale to assess resilience. Statistical analysis was performed using SPSS 28.0 software, conducting descriptive analyses, correlations, and hierarchical multiple linear regressions to examine the predictive capacity of the variables, and a 2×2 repeated-measures ANOVA (time × gender). The results showed significant increases in intrinsic motivation, enjoyment, self-confidence, and resilience after the intervention. Enjoyment emerged as the main predictor of intrinsic motivation, followed by self-confidence and resilience. Furthermore, the ANOVA revealed the significant effect of time whereas there were no significant differences between boys and girls, indicating that the program was equally effective for both genders.