Hyperacusis, a hypersensitivity to sounds of mild to moderate intensity, has been related to increased neural gain along the auditory pathway. To date, there is still uncertainty on the neural correlates of hyperacusis. Since hyperacusis often co-occurs with hearing loss and tinnitus, the effects of the three conditions on cortical and subcortical structures are often hard to separate. In this fMRI study, two groups of hearing loss and tinnitus participants, with and without hyperacusis, were compared to specifically investigate the effect of the latter in a group that often reports hyperacusis. In 35 participants with hearing loss and tinnitus, with and without hyperacusis as indicated by a cut-off score of 22 on the Hyperacusis Questionnaire (HQ), subcortical and cortical responses to sound stimulation were investigated. In addition, the frequency tuning of cortical voxels was investigated in the primary auditory cortex. In cortical and subcortical auditory structures, sound-evoked activity was higher in the group with hyperacusis. This effect was not restricted to frequencies affected by hearing loss but extended to intact frequencies. The higher subcortical and cortical activity in response to sound thus appears to be a marker of hyperacusis. In contrast, the response to the tinnitus frequency was reduced in the group with hyperacusis. This increase in subcortical and cortical activity in hyperacusis can be related to an increase in neural gain along the auditory pathway, and the reduced response to the tinnitus frequency to differences in attentional resources allocated to the tinnitus sound.