Niemann-Pick type C (NPC) disease is a devastating, fatal, neurodegenerative disease and a form of lysosomal storage disorder. It is caused by mutations in either NPC1 or NPC2 genes, leading to the accumulation of cholesterol and other lipids in the late endosome/lysosome system, a hallmark of the disease. Due to aberrant lipid trafficking in NPC, various techniques have been employed to study cholesterol and lipid dysregulation. Among them, mass spectrometry (MS)-based lipidomics has emerged as a state-of-the-art approach, providing valuable insights into disease pathophysiology, progression, and therapeutic target development. This review highlights the MS instruments used for lipidomics studies and discusses lipid biomarkers identified using MS in the context of NPC disease. Furthermore, integrating lipidomics with other -omics approaches, and leveraging the power of artificial intelligence, should be prioritized in future studies to holistically understand NPC disease.