The higher prevalence of affective symptoms among women compared to men emerges in adolescence, and it has been associated with pubertal maturation. However, it remains unclear whether pubertal timing has long-term influences on affective symptoms. Using data from the British 1946 birth cohort, we investigated whether pubertal timing was associated with affective symptoms over the life course, distinguishing those with symptoms in adolescence only, symptoms in adulthood only, and symptoms in both adolescence and adulthood. In females, there was no evidence that early pubertal maturation was a risk factor for affective symptoms. However, those with particularly late menarche (≥15 years) showed a lower risk of adult-onset affective symptoms (odds ratio = 0.54, 95% confidence interval = 0.31, 0.95). This effect of late pubertal timing was not explained by a range of sociobehavioral factors. In contrast, in males, late pubertal timing was associated with increased risk of adolescent-onset affective symptoms that tracked into adulthood (odds ratio = 2.10, 95% confidence interval = 1.44, 3.06). This effect was partly explained by low prepubertal body mass index. Sex-specific effects of pubertal timing on the long-term risk of affective symptoms might be due to different effects of gonadal hormonal on the central nervous system, as well as different social experiences during puberty.