This analysis examined the relative contributions of sex, age, body mass index (BMI), and puberty (Tanner) stage on salivary melatonin amplitude. Sixty-nine children and adolescents (30 females; 9.6–17.8 years) were examined for Tanner stage. Serial salivary melatonin samples were collected in controlled conditions, from which these melatonin amplitude measures were derived: area under the curve (AUC) and maximum value (MAX). AUC declined with advancing Tanner stage. This melatonin decline was similar between boys and girls, but girls secreted more melatonin compared to boys. Tanner stage and sex explained AUC variability, but age and BMI did not; similar results emerged for MAX. These results indicate that puberty stage may either mediate the decline of melatonin, or the decrease in melatonin amplitude may be an indicator of pubertal progression. These findings also indicate that the melatonin decline during puberty is not entirely accounted for by body mass or by age.