Quantum graphs with leads to infinity serve as convenient models for studying various aspects of systems which are usually attributed to chaotic scattering. They are also studied in several experimental systems and practical applications. In the present manuscript we investigate the effect of a time dependent random noise on the transmission of such graphs, and in particular on the resonances which dominate the scattering observable such as e.g., the transmission and reflection intensities. We model the noise by a potential αδ(x − (x 0 + γ(t))) localized at an arbitrary point x 0 on any of the graph bonds, that fluctuates in time as a Brownian particle bounded in a harmonic potential described by the Ornstein-Uhlenbeck statistics. This statistics, which binds the Brownian motion within a finite interval, enables the use of a second order time-dependent perturbation theory, which can be applied whenever the strength parameter α is sufficiently small. The theoretical frame-work will be explained in full generality, and will be explicitly solved for a simple, yet nontrivial example.