Background: Motivational climate in sport is a psychosocial construct which is related with several factors, such as healthy habits and well-being, and is influenced by teachers, trainers, and parents. The aim of this study was to assess the relationships between motivational climate, family functionality, and physical activity within a population of students from Spain and Romania. Methods: A cross-sectional study was conducted on a sample of university students specialization: physical education (n = 605; 20.71 ± 2.42 years old), using the perceived motivational climate in sport questionnaire-2 (PMCSQ-2), the physical activity questionnaire for adolescents (PAQ-A), and the family functionality scale (APGAR) as the main instruments. IBM SPSS Amos was used for data analysis in the structural equation model that was developed. Results: We observed positive relationships between task-oriented climate, family functionality, and the level of physical activity, showing higher regression weights for Spanish university students. Ego-oriented climate was negatively related to family functionality in Spanish university students, while this association was positive in Romanian students. Moreover, the relationship between physical activity and functional family was stronger in respondents from Spain. Conclusions: It can be pointed out that a better family functionality can promote higher levels of physical activity and self-determined motivations in sports shown by task-oriented motivational climates. Thus, it is essential to take into account the influence of family in the promotion of healthy lifestyles.