The positive association between heart rate variability and cardiorespiratory fitness in youth populations is unclear. In this regard, several methodological aspects related to heart rate variability analysis could partially explain the disagreement between studies. To the best of the authors’ knowledge, the influence of the heart rate on data analysis is unclear. In the present short communication, we discuss the impact of the heart rate on the associations between heart rate variability and cardiorespiratory fitness in youth. In addition, we proposed some aspects that should be considered for statistical analyses when the relationship between heart rate variability and cardiorespiratory fitness is studied. Finally, we should acknowledge that these recommendations may be applicable for other health-related outcomes different than cardiorespiratory fitness (e.g., inflammatory markers, cognition, cardiovascular disease status).