The flux averaging method which was introduced in order to calculate transmission probabilities in resonant tunneling processes is reformulated for calculations of thermal rate constants for reactions with long-lived intermediate states, associated with quantum resonances. The rate constant is expressed as a time-dependent weighted average of time integrals over different flux-flux correlation functions. This exact expression for the rate is shown to converge to its asymptotic value within the 'direct' dynamics timescale, regardless of the population of long-lived resonance states. The method is derived and demonstrated for symmetric and non-symmetric resonance-supporting double-barrier potentials. (C) 2003 Elsevier Science B.V. All rights reserved.