Human milk fat plays an essential role as the source of energy and cell function regulator; therefore, the preservation of unique human milk donors’ lipid composition is of fundamental importance. To compare the effects of high pressure processing (HPP) and holder pasteurization on lipidome, human milk was processed at 62.5 °C for 30 min and at five variants of HPP from 450 MPa to 600 MPa, respectively. Lipase activity was estimated with QuantiChrom™ assay. Fatty acid composition was determined with the gas chromatographic technique, and free fatty acids content by titration with 0.1 M KOH. The positional distribution of fatty acid in triacylglycerols was performed. The oxidative induction time was obtained from the pressure differential scanning calorimetry. Carotenoids in human milk were measured by liquid chromatography. Bile salt stimulated lipase was completely eliminated by holder pasteurization, decreased at 600 MPa, and remained intact at 200 + 400 MPa; 450 MPa. The fatty acid composition and structure of human milk fat triacylglycerols were unchanged. The lipids of human milk after holder pasteurization had the lowest content of free fatty acids and the shortest induction time compared with samples after HPP. HPP slightly changed the β-carotene and lycopene levels, whereas the lutein level was decreased by 40.0% up to 60.2%, compared with 15.8% after the holder pasteurization.