The purpose of this study is to present the numerical investigations of an infection-based fractional-order nonlinear prey-predator system (FONPPS) using the stochastic procedures of the scaled conjugate gradient (SCG) along with the artificial neuron networks (ANNs), i.e., SCGNNs. The infection FONPPS is classified into three dynamics, susceptible density, infected prey, and predator population density. Three cases based on the fractional-order derivative have been numerically tested to solve the nonlinear infection-based disease. The data proportions are applied 75%, 10%, and 15% for training, validation, and testing to solve the infection FONPPS. The numerical representations are obtained through the stochastic SCGNNs to solve the infection FONPPS, and the Adams-Bashforth-Moulton scheme is implemented to compare the results. The infection FONPPS is numerically treated using the stochastic SCGNNs procedures to reduce the mean square error (MSE). To check the validity, consistency, exactness, competence, and capability of the proposed stochastic SCGNNs, the numerical performances using the error histograms (EHs), correlation, MSE, regression, and state transitions (STs) are also performed.