Questionnaires aimed at assessing the prevalence of physical activity are tools frequently used by health professionals. It is important to provide them with information about the characteristics and quality of these questionnaires. This systematic review aimed to identify and analyse the characteristics and psychometric properties of this type of questionnaires when administered to Spanish children and adolescents. A total of 14 questionnaires were found. Accurate validity values were obtained in two of them. Only two questionnaires obtained a score >5 in the “Qualitative Attributes and Measurement Properties of Physical Activity Questionnaires” checklist. Among the available questionnaires, the APALQ (9-18 years) and the ENERGY (12-14 years) seem to be the most accurate tools for assessing physical activity prevalence in Spanish children and adolescents, albeit with limitations that should be taken into account.