Squalene epoxidase is a key enzyme involved in triterpene saponins biosynthetic pathways in plants. In this study, the SE gene was isolated from Ginkgo biloba by RT-PCR, which designated as GbSE, GenBank accession number: KY751713. The length of GbSE gene is 1646 bp, contains an open reading frame of 1617 bp encoding 538 amino acids. The theoretical molecular weight and pI of GbSE protein was 58.3 kDa and 8.35, respectively. Sequence multiple alignment found that GbSE protein had high homology with SE proteins from other plants, including several highly conservative motifs and amino acids. Phylogenetic tree analysis showed that Ginkgo biloba SE belonged to the gymnospermous group, and was closely related to the SE protein of Picea sitchensis. A study of gene expression analysis indicated that the GbSE gene was highly expressed in stems, low expressed in fruits. The cDNA sequence of GbSE gene was cloned from G. biloba and the expression level of this gene was analyzed. This work can provide some theoretical basis for the research on the molecular mechanism of triterpenoid saponin biosynthesis.