Comparative lipidomic studies were performed across the RT4 versus T24 urothelial cancer cell lines, as models for noninvasive urothelial papilloma cells (with a relatively high level of differentiation) and invasive urothelial carcinoma cells (with low level of differentiation), respectively. The aim was to investigate the differences in lipid profile associated with different levels of urothelial cancer cell invasiveness. The cellular lipidomes were characterized using our previously developed joint methodology of liquid chromatography-mass spectrometry and high-resolution nuclear magnetic resonance, which included analysis of the phospholipids and ceramide-based glycosphingolipids. This study shows that the invasive T24 cells have 3-fold lower levels of 1-alkyl (ether)-2-acyl phosphocholine species, which are accompanied by greater length and higher unsaturation of acyl chains of several lipid classes. Moreover, d18:1-based glycosphingolipids show different profiles; in particular, α-hydroxylated glucosylceramides have lower levels in the T24 cells, along with increased lactosyl ceramides. These differences between RT4 and T24 cells suggest significantly different organization of the cellular membranes, which can affect the membrane fluidity and membrane-dependent functions, and contribute to the lower stiffness of plasma membrane and reduced cell-cell adhesion required for movement and invasiveness of these T24 urothelial carcinoma cells with a high metastatic potential.