Fathers play a unique and important role in shaping their children’s physical activity (PA), independent from the mother. Lifestyle interventions focusing simultaneously on PA of fathers and their children (“co-PA”) are therefore a novel and promising way to improve PA of both. A theory-based lifestyle intervention was co-created with fathers (i.e., the Run Daddy Run intervention), using the behavior change wheel as a theoretical framework. The aim of the present study is to describe the protocol of the Run Daddy Run intervention study, focusing on improving (co-)PA of fathers and children, and the prospected outcomes. The developed intervention consists of six (inter)active father-child sessions and an eHealth component, delivered over a 14-week intervention period. Baseline measurements will be conducted between November 2019-January 2020, post-test measurements in June 2020, and follow-up measurements in November 2020, with (co-)PA as the primary outcome variable. Outcomes will be measured using accelerometry and an online questionnaire. To evaluate the intervention, multilevel analyses will be conducted. This study will increase our understanding on whether a theory-based, co-created lifestyle intervention focusing exclusively on fathers and their children can improve their (co-)PA behavior and has important implications for future research and health policy, where targeting fathers might be a novel and effective approach to improve (co-)PA and associated health behaviors of both fathers and their children.