Cancer metabolism is associated with enhanced lipogenesis required for rapid growth and proliferation. However, the magnitude of dysregulation of diverse lipid species mostly remains to be characterized, particularly in rare cancers such as ovarian clear cell carcinoma (OCCC). Here we implemented a robust sample preparation workflow together with targeted LC-MS/MS to identify the lipidomic changes in formalin-fixed paraffin-embedded specimen from OCCC as compared to uninvolved contralateral ovarian tissue. We quantitated 342 lipid species representing 28 lipid classes. We observed differential regulation of diverse lipid species belonging to several glycerophospholipid classes and trihexosylceramide. A number of unsaturated lipid species were increased whereas saturated lipid showed a decrease in OCCC as compared to the controls. We also carried out total fatty acid analysis and observed increase in the levels of several unsaturated fatty acids with concomitant increase in the index of stearoyl-CoA desaturase (SCD) in OCCC. We confirmed the upregulation of SCD, the rate-limiting enzyme for the synthesis of monounsaturated fatty acids, by immunohistochemistry (IHC) assays. Hence, by carrying out mass spectrometry analysis of archival tissue samples, we were able to provide novel insights into the lipidomic alterations of OCCC.