It is necessary to study hormonal patterns from mules to recognize alterations and neonatal maladaptation. Our objective was to evaluate concentrations of hormones in mule (n = 6) and equine foals (n = 6). Blood was collected at T0, 1, 6 and 12 h after birth. Hormone concentrations were evaluated using liquid chromatography tandem mass spectrometry. Effects of time, group and interactions and regression analysis were evaluated (p < 0.05). There was a cubic and quadratic decline in mule and equine foals, respectively, for 3β,20α-dihydroxy-DHP. Mule foals were born with lower circulating 3β,20α-dihydroxy-DHP concentrations, which might be related to progestogen concentrations in mares with a hybrid placenta. Corticosterone and cortisol concentrations remained unchanged for the first hour post-foaling then declined in mule and equine foals (p < 0.0001). Dehydroepiandrosterone was the main androgen present. There was a decrease in dihydrotestosterone at 12 h (p = 0.002). Differences in the temporal patterns of secretion within each steroid class, pregnanes, corticoids, and androgens, suggest they were derived from different tissue sources, presumptively the placenta, adrenals and gonads of the fetus/neonate, respectively. Mule and horse foals were born without evidence of testosterone secretion. For the first time, steroid hormone levels were measured in neonatal mules, and this will provide insight into neonatal physiology that differs from equine and allow us to gain an understanding of mules that have rarely been studied. Further studies are needed to elucidate the effects of hybrid pregnancies in the steroid endocrinology of neonates.