This manuscript describes the rationale and protocol of a school-based randomized controlled trial called “Cycling and Walk to School” (PACO, by its Spanish acronym) that aims to promote cycling to and from school and physical activity (PA) in adolescents. This study will examine the effects of this intervention in cycling and active commuting to and from school (ACS), PA and several ACS-related factors based on self-determination theory (SDT) and a social-ecological model (SEM). A total of 360 adolescents attending six high schools (three experimental and three control) from three Spanish cities will participate in this randomized controlled trial. The intervention (four cycling sessions; 1–2 h per session, one session per week) will be conducted by the research staff; the control group will continue their usual activities. PA levels will be measured by accelerometers, whereas ACS and the other study variables will be self-reported using questionnaires at baseline and post-intervention. The primary outcomes will be: rates of cycling to school, ACS and PA levels. In addition, SDT-related variables and individual, interpersonal, community, and environment variables relevant to ACS will be based on SEM. The findings will provide a comprehensive understanding of the short-term effects of this school-based intervention on cycling to school behaviour, ACS and PA levels in Spanish adolescents.