To explore the effects of pulsed electric field treatment on the germination of Scutellaria baicalensis seeds and the growth of seedlings, this study used the response surface methodology to design the working parameters of the pulsed electric field and treated and cultured Scutellaria baicalensis seeds. The results showed that the pulsed electric field treatment was beneficial for the germination of Scutellaria baicalensis seeds, improving the metabolic activity and stress resistance of seedlings. When the pulsed electric field treatment’s parameters were 0.5 kV·cm⁻¹, 120 μs, and 99 pulses, the germination potential of seeds was significantly increased by 29.25% and the germination index significantly increased by 20.65%, compared to the control. From 5th to 15th day, the activities of SOD, POD, and α-amylase in the seedlings, and the contents of Pro, soluble sugars, and soluble proteins were significantly increased, compared to the control. This study provides a theoretical basis for improving the germination and seedling growth of medicinal herbs such as Scutellaria baicalensis and their practical application in production.