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To explore the effects of pulsed electric field treatment on the germination of <i>Scutellaria baicalensis</i> 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 <i>Scutellaria baicalensis</i> seeds. The results showed that the pulsed electric field treatment was beneficial for the germination of <i>Scutellaria baicalensis</i> 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 <i>Scutellaria baicalensis</i> and their practical application in production.