Intolerance of uncertainty (IU) can influence emotional predictions, constructed by the brain (generation stage) to prearrange action (implementation stage), and update internal models according to incoming stimuli (updating stage). However, neurocomputational mechanisms by which IU affects emotional predictions are unclear. This high-density EEG study investigated if IU predicted event-related potentials (ERPs) and brain sources activity developing along the stages of emotional predictions, as a function of contextual uncertainty. Thirty-six undergraduates underwent a S1-S2 paradigm, with emotional faces and pictures as S1s and S2s, respectively. Contextual uncertainty was manipulated across three blocks, each with 100%, 75%, or 50% S1-S2 emotional congruency. ERPs, brain sources and their relationship with IU scores were analyzed for each stage. IU did not affect prediction generation. During prediction implementation, higher IU predicted larger Contingent Negative Variation in the 75% block, and lower left anterior cingulate cortex and supplementary motor area activations. During prediction updating, as IU increased P2 to positive S2s decreased, along with P2 and Late Positive Potential in the 75% block, and right orbito-frontal cortex activity to emotional S2s. IU was therefore associated with altered uncertainty assessment and heightened attention deployment during implementation, and to uncertainty avoidance, reduced attention to safety cues and disrupted access to emotion regulation strategies during prediction updating.