© 2018 Elsevier B.V. Previous EEG-ERP dynamics studies found non-random “preferred” EEG phases at stimulus onset in a fixed interstimulus interval (ISI) equiprobable auditory Go/NoGo paradigm, with substantial effects on ERP components. Here we changed to a variable ISI task to prevent/reduce preferential phase occurrence. Discrete Fourier transforms decomposed prestimulus EEG at Cz for each trial to calculate the phase of different frequencies at stimulus onset; we combined these into the delta, theta, alpha, and beta bands, and then sorted trials into phase quartiles for each. ERPs from the raw EEG, assessed using temporal Principal Components Analyses, were examined as a function of phase at stimulus onset. Preferential phase occurrence was reduced as predicted, but random phase substantially impacted component amplitudes. For example, negativity in delta enhanced Go and NoGo P3b; and in theta reduced NoGo but not Go P3b. Overall, EEG phases at stimulus onset support differential cognitive processing in this two-choice task.