There is broad scientific evidence on the health benefits of omega-3 polyunsaturated fatty acids (n-3 PUFAs), especially docosahexaenoic acid (DHA, 22:6n3) and eicosapentaenoic acid (EPA, 20:5n3). On the other hand, polar lipids (phospholipids, PLs, and glycolipids, GLs) are excellent emulsifying agents, making them useful both as food products and as excipients for drugs and cosmetics. The bioavailability of n-3 PUFAs in the form of PLs is greater than that of ethyl esters and triacylglycerols. This work has developed an easy method for the simultaneous extraction and fractionation of saponifiable lipids (SLs) from the microalga Nannochloropsis sp., using low-toxicity solvents. Firstly, a lipidic fraction very rich in neutral saponifiable lipids (NSLs) was obtained using hexane. Next, an EPA and polar lipids (PLs and GLs)-enriched fraction was obtained using ethanol (96%). Under optimal conditions, in the first extraction with hexane, an SL extract with 86.3% NSLs was obtained; this extract contained 88.9% of the biomass NSLs. Subsequently, in the second extraction step with ethanol (96%), an SL extract with 87.1% polar lipids and up to 35.2% EPA was obtained. This SL extract contained 87.1% of the polar lipids and 74.7% of the EPA from the Nannochloropsis sp. biomass.