Intracellular biochemical networks often display large fluctuations in the molecule numbers or the concentrations of reactive species, making molecular approaches necessary for system descriptions. For Markovian reaction networks, the fluctuation-dissipation theorem (FDT) has been well established and extensively used in fast evaluation of fluctuations in reactive species. For non-Markovian reaction networks, however, the similar FDT has not been established so far. Here, we present a generalized FDT (gFDT) for a large class of non-Markovian reaction networks where general intrinsic-event waiting-time distributions account for the effect of intrinsic noise and general stochastic reaction delays represent the impact of extrinsic noise from environmental perturbations. The starting point is a generalized chemical master equation (gCME), which describes the probabilistic behavior of an equivalent Markovian reaction network and identifies the structure of the original non-Markovian reaction network in terms of stoichiometries and effective transition rates (extensions of common reaction propensity functions). From this formulation follows directly the solution of the linear noise approximation of the stationary gCME for all the components in the non-Markovian reaction network. While the gFDT can quickly trace noisy sources in non-Markovian reaction networks, example analysis verifies its effectiveness.