Prior knowledge of the probabilities concerning decision alternatives facilitates the selection of more likely alternatives to the disadvantage of others. The neural basis of prior probability (PP) integration into the decision-making process and associated preparatory processes is, however, still essentially unknown. Furthermore, trial-to-trial fluctuations in PP processing have not been considered thus far. In a previous study, we found that the amplitude of the contingent negative variation (CNV) in a precueing task is sensitive to PP information (Scheibe et al., 2009). We investigated brain regions with a parametric relationship between neural activity and PP and those regions involved in PP processing on a trial-to-trial basis in simultaneously recorded electroencephalographic (EEG) and functional magnetic resonance imaging (fMRI) data. Conventional fMRI analysis focusing on the information content of the probability precue revealed increasing activation of the posterior medial frontal cortex with increasing PP, supporting its putative role in updating action values. EEG-informed fMRI analysis relating single-trial CNV amplitudes to the hemodynamic signal addressed trial-to-trial fluctuations in PP processing. We identified a set of regions mainly consisting of frontal, parietal, and striatal regions that represents unspecific response preparation on a trial-to-trial basis. A subset of these regions, namely, the dorsolateral prefrontal cortex, the inferior frontal gyrus, and the inferior parietal lobule, showed activations that exclusively represented the contributions of PP to the trial-to-trial fluctuations of the CNV.