The modelling of linear quadratic Gaussian optimal control problems on large complex networks is intractable computationally. Graphon theory provides an approach to overcome these issues by defining limit objects for infinite sequences of graphs permitting one to approximate arbitrarily large networks by infinite dimensional operators. This is extended to stochastic systems by the use of Q-noise, a generalization of Wiener processes in finite dimensional spaces to processes in function spaces. The optimal control of linear quadratic problems on graphon systems with Q-noise disturbances are defined and shown to be the limit of the corresponding finite graph optimal control problem. The theory is extended to low rank systems, and a fully worked special case is presented. In addition, the worst-case long-range average and infinite horizon discounted optimal control performance with respect to Q-noise distribution are computed for a small set of standard graphon limits.