The low rates of active commuting to/from school in Spain, especially by bike, and the wide range of cycling interventions in the literature show that this is a necessary research subject. The aims of this study were: (1) to assess the feasibility of a school-based cycling intervention program for adolescents, (2) to analyse the effectiveness of a school-based cycling intervention program on the rates of cycling and other forms of active commuting to/from school (ACS), and perceived barriers to active commuting in adolescents. A total of 122 adolescents from Granada, Jaén and Valencia (Spain) participated in the study. The cycling intervention group participated in a school-based intervention program to promote cycling to school during Physical Education (PE) sessions in order to analyse the changes in the dependent variables at baseline and follow up of the intervention. Wilcoxon, Signs and McNemar tests were undertaken. The association of the intervention program with commuting behaviour, and perceived barriers to commuting, were analysed by binary logistic regression. There were improvements in knowledge at follow-up and the cycling skill scores were medium-low. The rates of cycling to school and active commuting to/from school did not change, and only the “built environment (walk)” barrier increased in the cycling group at follow-up. School-based interventions may be feasibly effective tools to increase ACS behaviour, but it is necessary to implement a longer period and continue testing further school-based cycling interventions.