To enhance the production of flavonoids [baicalin, wogonin-7-Ο-glucuronic acid (GA)], which are secondary metabolites of Scutellaria baicalensis Georgi(G.) plant cells, a multilayer perceptron control system was applied to regulate the substrate feeding in a fed-batch cultivation. The optimal profile for the substrate feeding rate in a fed-batch culture of S. baicalensis G. was determined by simulating a kinetic model using a genetic algorithm. Process variable profiles were then prepared for the construction of a multilayer perceptron controller that included massive parallelism, trainability, and fault tolerance. An error back-propagation algorithm was applied to train the multiplayer perceptron. The experimental results showed that neurocontrol incorporated with a genetic algorithm improved the flavonoid production compared with a simple fuzzy logic control system. Furthermore, the specific production yield and flavonoid productivity also increased.