Thyroid hormones (THs) induce metamorphosis in amphibians, causing dynamic changes, whereas mammalian newborns undergo environmental transition from placenta to open air at birth. The similarity between amphibian metamorphosis and the mammalian perinatal periods has been repeatedly discussed. However, a corresponding developmental gene expression analysis has not yet been reported. In this study, we examined the developmental gene expression profiles in the brain and liver of Xenopus tropicalis during metamorphosis climax and compared them to the respective gene expression profiles of newborn rodents. Many upregulated genes identified in the tadpole brain during metamorphosis are also upregulated in the rodent brain during the first three postnatal weeks when the TH surge occurs. The upregulation of some genes in the brain was inhibited in thyroid hormone receptor α (TRα) knockout tadpoles but not in TRβ-knockout tadpoles, implying that brain metamorphosis is mainly mediated by TRα. The expression of some genes was also increased in the liver during metamorphosis climax. Our data suggest that the rodent brain undergoes TH-dependent remodeling during the first three postnatal weeks as observed in X. tropicalis during the larva-to-adult metamorphosis.