Hundreds of specimens of the beaked bird Confuciusornis sanctus have been recovered from Early Cretaceous lake deposits of northeastern China. These birds show remarkable variation in size and plumage, with some displaying two long, central ornamental rectrices (tail feathers) and others lacking them altogether. Although, traditionally specimens with ornamental rectrices were interpreted as males and those without them as females, this supposed sexual dimorphism has remained unconfirmed. Here we report on the discovery of medullary bone, a tissue unique to reproductively active female birds, in a specimen of C. sanctus (DNHM-D1874) lacking these feathers. Our discovery constitutes the first case of gender identification in a Mesozoic bird, and it provides undisputed evidence that individuals of C. sanctus without ornamental rectrices are females. By permitting gender identification in C. sanctus, our results provide insight into the onset of sexual maturity and attainment of adult body size of this and other early birds.