Purpose: To provide safe and high-quality physical education, this study analyzed a physical literacy school-based intervention on active transport to school. Method: A total of 185 pupils (agemean = 11.76 ± 0.52; 46% girls) participated in the intervention. Pupils from test (n = 110) and control (n = 75) groups completed a survey based on their perceptions of the four dimensions of physical literacy (physical, cognitive, psychological, and social). Results: The test group displayed a significantly higher level of overall physical literacy compared with the control group (14.9 vs. 13.4) and also in the specific physical (16.4 vs. 15.3), cognitive (16.0 vs. 12.8), and psychological (15.3 vs. 13.8) dimensions. Boys recorded a significantly higher score than girls (16.7 vs. 14.5), particularly in the test group where girls showed less improvement than boys compared with the control group (+2.78 vs. +1.76). Discussion/Conclusion: Physical literacy is a dynamic process, which may be useful to reinforce the importance of incorporating this concept into physical education lesson planning while focusing on gender differences.