We propose a method utilizing physics-informed neural networks (PINNs) to solve Poisson equations that serve as control variates in the computation of transport coefficients via fluctuation formulas, such as the Green--Kubo and generalized Einstein-like formulas. By leveraging approximate solutions to the Poisson equation constructed through neural networks, our approach significantly reduces the variance of the estimator at hand. We provide an extensive numerical analysis of the estimators and detail a methodology for training neural networks to solve these Poisson equations. The approximate solutions are then incorporated into Monte Carlo simulations as effective control variates, demonstrating the suitability of the method for moderately high-dimensional problems where fully deterministic solutions are computationally infeasible.