This study proposes a system identification technique for a fiber-reinforced polymer deck with neural networks. Neural networks are trained for system identification and the identified structure gives training data in return. This process is repeated until the identified parameters converge. Hence, the proposed algorithm is called an iterative neural network scheme. The proposed algorithm also relies on recent developments in the experimental design of the response surface method. The proposed strategy is verified with known systems and applied to a fiber-reinforced polymer bridge deck with experimental data.