Temporal and spatial characteristics of fixations are affected by image properties, including high-level scene characteristics, such as object-background composition, and low-level physical characteristics, such as image clarity. The influence of these factors is modulated by the emotional content of an image. Here, we aimed to establish whether brain correlates of fixations reflect these modulatory effects. To this end, we simultaneously scanned participants and measured their eye movements, while presenting negative and neutral images in various image clarity conditions, with controlled object-background composition. The fMRI data were analyzed using a novel fixation-based event-related (FIBER) method, which allows the tracking of brain activity linked to individual fixations. The results revealed that fixating an emotional object was linked to greater deactivation in the right lingual gyrus than fixating the background of an emotional image, while no difference between object and background was found for neutral images. We suggest that deactivation in the lingual gyrus might be linked to inhibition of saccade execution. This was supported by fixation duration results, which showed that in the negative condition, fixations falling on the object were longer than those falling on the background. Furthermore, increase in the image clarity was correlated with fixation-related activity within the lateral occipital complex, the structure linked to object recognition. This correlation was significantly stronger for negative images, presumably due to greater deployment of attention towards emotional objects. Our eye-tracking results are in line with these observations, showing that the chance of fixating an object rose faster for negative images over neutral ones as the level of noise decreased. Overall, our study demonstrated that emotional value of an image changes the way that low and high-level scene properties affect the characteristics of fixations. The fixation-related brain activity is affected by the low-level scene properties and this impact differs between negative and neutral images. The high-level scene properties also affect brain correlates of fixations, but only in the case of the negative images.