Uncertainty has been shown to impact political evaluation, yet the exact mechanisms by which uncertainty affects the minds of citizens remain unclear. This experiment examines the neural underpinnings of uncertainty in political evaluation using functional MRI (fMRI). During fMRI, participants completed an experimental task where they evaluated policy positions attributed to hypothetical political candidates. Policy positions were either congruent or incongruent with candidates' political party affiliation and presented with varying levels of certainty. Neural activity was modelled as a function of uncertainty and incongruence. Analyses suggest that neural activity in brain regions previously implicated in affective and evaluative processing (anterior cingulate cortex, insular cortex) differed as a function of the interaction between uncertainty and incongruence, such that activation in these areas was greatest when information was both certain and incongruent and uncertainty influenced processing differently as a function of the valence of the attached information. These findings suggest that individuals are attuned to uncertainty in the stated issue positions of politicians, and that the neural processing of this uncertainty is dependent on congruence of these positions with expectations based on political party identification. Implications for the study of emotion and politics and political cognition are discussed.This article is part of the theme issue ‘The political brain: neurocognitive and computational mechanisms’.