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Physical activity has a demonstrated positive effect on youth depressive symptoms. However, very few studies have explored the bi-directionality of the links between physical activity and depression. The present study aims at filling this gap and tests whether any associations are moderated by sex. Moreover, the role of subtype of depressive symptoms, vegetative (i.e., lack of energy, poor sleep) or non-vegetative (i.e., mood-related), is explored. Participants were 910 12–13 year-old Swedish adolescents (56% girls) who answered a three-wave survey at ages 12–13 (T1), 15–16 (T2), and 18–19 (T3). Using a cross-lagged structural model, depression predicted decreased frequency of vigorous physical activity (VPA) from T1 to T2 (β = −0.09, p <.05) and from T2 to T3 (β = −0.10, p <.01), while frequency of VPA at T2 decreased depression at T3 (β = −0.12, p <.05). Associations did not differ between boys and girls. Non-vegetative symptoms predicted decreased frequency of VPA from T1 to T2 (β = −0.10, p <.05), while frequency of VPA at T2 predicted decreased non-vegetative symptoms at T3 (β = −0.15, p <.05). Vegetative symptoms predicted decreased frequency of VPA from T1 to T2 (β = −0.09, p <.05), while have a reciprocal influence with VPA from T2 to T3. Overall, our results highlight an association across adolescence between VPA and depression. The association becomes stronger and reciprocal in middle adolescence, which suggests this period as an effective developmental time to plan physical-activity-based interventions to decrease youth depressive symptoms.