Cell surface glycans show dynamic changes during cell differentiation. Several glycans are useful biomarkers of tumors, stem cells, and embryogenesis. Glycomic studies have been performed using liquid chromatography and mass spectrometry, which are powerful tools for glycan structural analysis but are difficult to use for small sample sizes. Recently, a lectin microarray system was developed for profiling cell surface glycome changes to terminal carbohydrate chains and branch types, using sample sizes of a few micrograms. In this study, we used the lectin microarray system for the first time to investigate stage-specific glycomes in Xenopus laevis embryos. Unsupervised cluster analysis of lectin microarray data indicated that glycan profiles changed sequentially during development. Nine lectin probes showed significantly different signals between early and the late-stage embryos: 4 showed higher signals in the early stages, and 5 exhibited higher signals in the late stages. The gene expression profiles of relevant glycosyltransferase genes support the lectin microarray data. Therefore, we have shown that lectin microarray is an effective tool for high-throughput glycan analysis in Xenopus embryogenesis, allowing glycan profiling of early embryos and small biopsy specimens.