Perceptual judgments are frequently made during uncertain situations. Previous human brain imaging studies have revealed multiple cortical and subcortical areas that are activated when decision uncertainty is linked to outcome probability. However, the neural mechanisms of uncertainty modulation in different perceptual decision tasks have not been systematically investigated. Uncertainty of perceptual decision can originate either from highly similar object categories (e.g. tasks based on criterion comparison) or from noise being added to visual stimuli (e.g. tasks based on signal detection). In this study, we used functional magnetic resonance imaging (fMRI) to investigate the neural mechanisms of task-dependent modulation of uncertainty in the human brain during perceptual judgements. We observed correlations between uncertainty levels and fMRI activity in a network of areas responsible for performance monitoring and sensory evidence comparison in both tasks. These areas are associated with late stages of perceptual decision, and include the posterior medial frontal cortex, dorsal lateral prefrontal cortex, and intraparietal sulcus. When the modulation of uncertainty on the two tasks was compared, dissociable cortical networks were identified. Uncertainty in the criterion comparison task modulated activity in the left lateral prefrontal cortex related to rule retrieval. In the signal detection task, uncertainty modulated activity in higher visual processing areas thought to be sensory information ‘accumulators’ that are active during early stages of perceptual decision. These findings offer insights into the mechanism of information processing during perceptual decision-making.