Lipofuscin is an autofluorescent storage material that accumulates in the brain with normal aging. Lipofuscin deposition is also observed in numerous disease states but is most profound in neuronal ceroid lipofuscinoses (NCLs), a group of fatal neurodegenerative disorders that primarily affect children. Lipofuscin is known to be generally composed of proteins, lipids, metals, and carbohydrates, yet few specific lipofuscin constituents have been elucidated. Further, the spatiotemporal progression of lipofuscin accumulation in murine models remains unclear. An improved molecular and neuroanatomical understanding of lipofuscin accumulation is needed to assess the relationship of this pathological hallmark to aging and neurodegenerative processes. To unveil regional vulnerabilities to lipofuscin accumulation, we generated a fine neuroanatomical atlas of lipofuscin in the aging and NCL brain. To identify lipofuscin constituents and dissect proteostatic, metabolic, and lipidation pathways related to lipofuscin biogenesis, we conducted a multimodal mass spectrometric analysis of purified and in situ lipofuscin. Our study offers a rich proteomic, lipidomic, small-molecule, and neuroanatomical description of lipofuscin in aging and NCL with diverse etiological implications.