The present study is to investigate the Gudermannian neural networks (GNNs) using the optimization procedures of genetic algorithm and active-set approach (GA-ASA) to solve the three-species food chain nonlinear model. The three-species food chain nonlinear model is dependent upon the prey populations, top-predator, and specialist predator. The design of an error-based fitness function is presented using the sense of the three-species food chain nonlinear model and its initial conditions. The numerical results of the model have been obtained by exploiting the GNN-GA-ASA. The obtained results through the GNN-GA-ASA have been compared with the Runge–Kutta method to substantiate the correctness of the designed approach. The reliability, efficacy and authenticity of the proposed GNN-GA-ASA are examined through different statistical measures based on single and multiple neurons for solving the three-species food chain nonlinear model.