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Because the offspring of parents with an affective disorder (OAD) are at high risk for developing mental disorders, and persons with an affective disorder (AD) show dysfunctional hypothalamic-pituitary-adrenal (HPA) axis activity, changes in HPA functioning in OAD might be an etiological risk factor that precedes the development of ADs. The primary aim of the meta-analysis was to quantitatively summarize the existing data on different indices of diurnal cortisol in the OAD. The secondary aim was to explore potential moderators of this relation. Following PRISMA guidelines, we included 26 studies (3052 offspring) on diurnal cortisol in our meta-analysis after an initial screening of 3408 articles. Intercept-only and meta-regression models were computed using the robust variance estimation method. Analyses examining mean cortisol levels at discrete timepoints, total cortisol output, and the cortisol rise in response to awakening (CAR) were conducted separately. The results demonstrated that the OAD had higher mean levels of cortisol at different timepoints throughout the day compared to controls (Hedge's g = 0.21). There was evidence of publication bias in studies examining CAR, such that effect sizes were positively biased. The present findings are consistent with a meta-analysis showing elevated cortisol in youth having an AD. Notable limitations across studies include the method of cortisol measurement and assessment of ADs. Altogether, these results highlight the fact that increased cortisol levels may act as a potential neuroendocrine antecedent and/or risk factor for the development of ADs among high risk youth.