Background: Adolescence is a decisive stage in human development during which intense physical, psychological, emotional and social changes are experienced. The aim of the present study was to analyse the lifestyle differences related with the health of adolescents enrolled in first year (13.01 ± 0.62 years old) and fourth year of secondary education (16.02 ± 0.63 years old) from a region in the North of Spain. Method: A cross-sectional study was conducted with a sample of 761 adolescents from twenty-five educational centres in a northern region of Spain. The sample was made up of 383 first year students and 378 fourth year students. Physical activity engagement, health-related quality of life, self-esteem, adherence to a Mediterranean diet, hours of nightly sleep, body mass index and maximum oxygen consumption were evaluated. Results: First-year adolescent students reported higher values for self-esteem, health-related quality of life, physical activity, Mediterranean diet adherence, hours of nightly sleep and maximal oxygen consumption. Some differences emerged according to sex. Associative analysis revealed negative correlations between age, lifestyle habits (physical activity engagement, hours of nightly sleep and Mediterranean diet adherence) and health indicators (VO2max, self-esteem and HRQoL), with a positive association emerging with BMI. Similar findings emerged regardless of sex, with the exception of findings pertaining to VO2max not being significant in boys. Conclusion: Differences perceived as a function of the adolescent’s age suggest that it should be an important consideration for educational and health organisations, with the aim of establishing intervention strategies appropriate for each age group.