Objectives This study aimed to: (1) model changes in the hypertensive and waist phenotype (HWP) in youth, and (2) investigate the effects of sex, biological maturation, total physical activity (TPA), and physical fitness (PF) in HWP trajectories. Methods Data were obtained annually for 3 years from the Oporto Growth, Health, and Performance Study, and comprised 5,549 adolescents (2,732 girls) divided into four age cohorts (10, 12, 14, and 16 years). The HWP was computed as the sum of the standardized score of waist circumference and mean arterial pressure. Biological maturation was indirectly assessed by the maturity offset procedure; TPA was estimated with the Baecke questionnaire; PF measures included 1‐mile run/walk, 50‐yard dash (50YD), standing long jump (SLJ), handgrip strength (HGr), and agility shuttle run. Longitudinal changes in HWP were analyzed using multilevel modelling. Results HWP increased across time with a nonlinear trend in girls and boys. However, when adjusted for a set of predictors, the trend was reversed: girls and boys had a significant annual decrease on HWP of −0.202 ± 0.032 and −0.147 ± 0.032, respectively. Maturity offset was positively associated with HWP changes (β = 0.913 ± 0.023); TPA had a negative association (β = −0.027 ± 0.011); and improved PF tests were associated with a significant reduction in HWP across time (β1mile = −0.081 ± 0.009; βSLJ = −0.003 ± 0.00; β50YD=0.106 ± 0.020; and βHGr = −3.335 ± 0.196). Conclusions Boys showed higher HWP values compared to girls from 10 to 18 years of age. Adolescents who were more biologically mature had a more adverse HWP. Longitudinal increases in TPA and PF predicted annual decreases in HWP across the adolescence years.Am. J. Hum. Biol. 28:387–393, 2016. © 2015 Wiley Periodicals, Inc.