Stimulus visibility is associated with neural signals in multiple brain regions, ranging from visual cortex to prefrontal regions. Here we used functional magnetic resonance imaging (fMRI) to investigate to which extent the perceived visibility of a “low-level” grating stimulus is reflected in the brain activity in high-level brain regions. Oriented grating stimuli were presented under varying visibility conditions created by backward masking. Visibility was manipulated using four different stimulus onset asynchronies (SOAs), which created a continuum from invisible to highly visible target stimuli. Brain activity in early visual areas, high-level visual brain regions (fusiform gyrus), as well as parietal and prefrontal brain regions was significantly correlated with subjects' psychometric visibility functions. In addition, increased stimulus visibility was reflected in the functional coupling between low and high-level visual areas. Specifically, neuroimaging signals in the middle occipital gyrus were significantly more correlated with signals in the inferior temporal gyrus when subjects successfully perceived the target stimulus than when they did not. These results provide evidence that not only low-level visual but also high-level brain regions reflect visibility of low-level grating stimuli and that changes in functional connectivity reflect perceived stimulus visibility.