The adoption of active travel (AT) habits in adolescence, supported by positive emotions, increases the chances of a lifelong positive attitude towards AT. The aim of this study was to assess the associations between active travel and well-being (WB), and to estimate the share of AT in weekly physical activity (PA) and its contribution to meeting the weekly PA recommendations in adolescents. The International Physical Activity Questionnaire-long form and the WHO-5 questionnaire were used to assess the level of AT, weekly PA and well-being of 2805 adolescents from 36 Czech and 39 Polish schools. A higher rate of AT is only significantly associated with higher well-being in girls. However, meeting AT recommendations in combination with higher WB increased the likelihood of meeting the weekly PA recommendations in both girls and boys. AT accounts for 22.5% of weekly PA of Czech (Polish 24.2%) boys. Concerning girls, it accounts for 24.9% of weekly PA in the Czech Republic and 24.5% in Poland. Meeting AT recommendations should be part of comprehensive school-based PA programs. State, school and municipal policies in the Central European region should pay more attention to the improvement of WB and the built environment for AT in secondary school adolescents.