The aim of the current study was modeling and optimizing medium compositions for shoot proliferation of chrysanthemum, as a case study, through radial basis function- non-dominated sorting genetic algorithm-II (RBF-NSGAII). RBF as one of the artificial neural networks (ANNs) was used for modeling four outputs including proliferation rate (PR), shoot number (SN), shoot length (SL), and basal callus weight (BCW) based on four variables including 6-benzylaminopurine (BAP), indole-3-butyric acid (IBA), phloroglucinol (PG), and sucrose. Afterward, models were linked to the optimization algorithm. Also, sensitivity analysis was applied for evaluating the importance of each input. The R2 correlation values of 0.88, 0.91, 0.97, and 0.76 between observed and predicted data were obtained for PR, SN, SL, and BCW, respectively. According to RBF-NSGAII, optimal PR (98.85%), SN (13.32), SL (4.83 cm), and BCW (0.08 g) can be obtained from a medium containing 2.16 µM BAP, 0.14 µM IBA, 0.29 mM PG, and 87.63 mM sucrose. The results of sensitivity analysis indicated that PR, SN, and SL were more sensitive to BAP, followed by sucrose, PG, and IBA. Finally, the performance of predicted and optimized medium compositions were tested, and results showed that the difference between the validation data and RBF-NSGAII predicted and optimized data were negligible. Generally, RBF-NSGAII can be considered as an efficient computational strategy for modeling and optimizing in vitro organogenesis.