Sea urchins (Echinodermata, Echinoidea) are good a source of bioactive compounds belonging to different classes of natural substances. The edible Mediterranean sea urchin Paracentrotus lividus is a renowned animal model for study in different fields of biology, but it is intensively harvested for high commercial value due to the delicacy of its gonads. Most studies have focused on the composition and the nutritional value of P. lividus gonads (the edible part), but little interest has been taken in the other body parts, such as the shells and spines, which are generally considered waste material. The purpose of this study was to obtain an extract from sea urchin shells, with a green methodology of extraction, and to characterize the lipophilic components for potential applications. The shells of P. lividus were extracted via a very well performing technology based on rapid solid liquid dynamic extraction (RSLDE) implemented via an automated device (Naviglio Extractor®). The obtained extract shows the presence of fatty acids and their esters (methyl, ethyl and 1-glycerol esters). Gas chromatography-mass spectrometry (GC-MS) measurements were used to determine fatty acid abundance in the chromatographic fractions of the extract. Arachidonic acid (ARA), 5,8,11,14,17-eicosapentanoic acid (EPA), and 11-eicosenoic acids and their esters are the most abundant components. The presence of many polyunsaturated fatty acids (PUFA) in the extract, even in low percentages allows a future application in nutrition or medical use.