Childhood adversity has been associated with hypothalamic–pituitary–adrenal axis dysregulation, which is associated with mental and physical health consequences. However, associations between childhood adversity and cortisol regulation in the current literature vary in magnitude and direction. This multilevel meta-analysis examines the association between childhood adversity and diurnal cortisol measures, as well as potential moderators of these effects (adversity timing and type, study or sample characteristics). A search was conducted in online databases PsycINFO and PubMed for papers written in English. After screening for exclusion criteria (papers examining animals, pregnant women, people receiving hormonal treatment, people with endocrine disorders, cortisol before age 2 months, or cortisol after an intervention), 303 papers were identified for inclusion. In total, 441 effect sizes were extracted from 156 manuscripts representing 104 studies. A significant overall effect was found between childhood adversity and bedtime cortisol, r = 0.047, 95% CI [0.005, 0.089], t = 2.231, p = 0.028. All other overall and moderation effects were not significant. The lack of overall effects may reflect the importance of the timing and nature of childhood adversity to adversity’s impact on cortisol regulation. Thus, we offer concrete recommendations for testing theoretical models linking early adversity and stress physiology.