Given that physical activity (PA) plays an important role in early childhood, understanding the factors that affect the practice of PA at an early age could help develop effective strategies for overcoming barriers and increasing activity levels in this age group. A qualitative study was conducted based on grounded theory aimed at exploring the perceptions of mothers and fathers from Cuenca and Ciudad Real (Castilla La Mancha, Spain) regarding barriers and facilitators of physical activity of their children during the adiposity rebound period. Data were collected using focus groups involving 46 parents of children in the 3rd grade of pre-school and 1st grade of elementary school. During the analysis, the socio-ecological model and grounded theory were used. The barriers encountered were the preferences of children for sedentary activities (individual factors), academic tasks as a main priority of parents, the influence of older siblings and the unfavorable school environment (microsystem), the lack of family conciliation (mesosystem), and barriers related to the built environment or lack of facilities for physical activity (exosystem). Facilitators were the preferences for active games (individual factors), parental models including the co-participation of parents in activities, the influence of friends, living in large homes, the support provided by teachers and the school (microsystem), living in rural areas, having sufficient facilities, favorable weather conditions (exosystem), and the existence of free or subsidized activities (macro system). Programs aimed at promoting PA in early childhood should include strategies that address contextual factors and not only focus on individual factors related to the child.