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Hyperacusis is a condition marked by increased sensitivity to everyday sounds, often resulting in discomfort, pain, and social withdrawal. Despite its significant impact on mental well-being and quality of life, the underlying neural mechanisms remain poorly understood. This systematic review evaluates magnetic resonance imaging (MRI)-based studies investigating structural, functional, and connectivity-related brain changes in individuals with hyperacusis. A total of 11 studies were included, using structural MRI (sMRI), functional MRI (fMRI), and diffusion tensor imaging (DTI). Functional MRI studies consistently reported increased neural activity in key auditory regions such as Heschl’s gyrus, superior temporal gyrus, and the parahippocampal area. These findings were associated with high standardised mean differences (SMDs >5.0), reflecting exaggerated auditory processing. Structural MRI findings showed reduced grey matter volume, particularly in the right supplementary motor area, with large SMDs (e.g., SMD = 2.10), suggesting impaired sound modulation mechanisms. DTI studies highlighted altered integrity of auditory pathways, including the medial geniculate nucleus and inferior colliculus, supporting the presence of disrupted connectivity. Subgroup analyses revealed modality-specific effects, with sMRI emphasising cortical alterations and fMRI capturing network-level hyperactivity. High heterogeneity in pooled estimates was attributed to differences in imaging protocols, study designs, and analysis methods. Sensitivity analyses helped stabilise the findings by accounting for extreme values. The review concludes that hyperacusis is a complex, multisystem condition involving both auditory and emotional processing networks. These findings underline the importance of adopting integrated diagnostic protocols and multidisciplinary therapeutic strategies targeting neural, emotional, and perceptual dysfunctions.