Inequalities in access to important resources and opportunities between social groups persist throughout societies worldwide. Social psychological research has shown that adults often use meritocratic beliefs to justify the existence of such inequalities. Yet, the developmental origins of meritocratic beliefs have yet to be fully explored. This study investigated how children and young adults (N = 144; 5- to 6-year-olds, M = 5.83, SD = 0.97; 9- to 11-year-olds, M = 10.74, SD = 0.68; 18- to 22-year-olds, M = 19.92, SD = 1.10) factored information about merit into their moral judgments and reasoning about science education resource inequalities between groups of girls and boys. Confirming our hypotheses, participants overall judged inequalities that disadvantaged high-merit groups more negatively than inequalities that disadvantaged low-merit groups, regardless of which gender group was disadvantaged. Further, exploratory analyses revealed age-related differences in judgments of inequalities that disadvantaged girls, but not boys. Whereas all age groups judged inequalities that disadvantaged boys more negatively when boys were described as high-merit compared to low-merit, only older children judged inequalities that disadvantaged girls more negatively when girls were described as high-merit compared to low-merit. Age-related differences also emerged for participants' reasoning about inequalities, such that older children were more likely to reason about merit, and less likely to reason about equality, compared to both younger children and young adults. These novel findings offer insights into how concerns for merit shape individuals' moral judgments of social inequalities throughout childhood and young adulthood.