Rare earth elements (REEs) have been widely used to increase accumulation of biomass and secondary metabolites in medicinal plants in China. However, very few studies have investigated how REEs mediate secondary metabolism synthesis in medicinal plants. Lanthanum (La), an important REE, is known to improve the accumulation of secondary metabolites in medicinal plants and is widely distributed in China. However, few studies have evaluated the signal transduction leading to La-induced secondary metabolism in medicinal plants. In this study, LaCl(3) treatment-induced multiple responses in Scutellaria baicalensis seedlings, including the rapid generation of jasmonic acid (JA), sequentially followed by the enhancement of baicalin production. Direct application of JA also promoted the synthesis of baicalin in the absence of LaCl(3). LaCl(3)-induced baicalin synthesis was blocked by two different JA synthesis inhibitors. Our results showed that JA acts as a signal component within the signaling system leading to La-induced baicalin synthesis in S. baicalensis seedlings.