Recently the miniaturization of liquid chromatography (LC) systems and progresses in mass spectrometry instrumentation have enabled direct introduction of the effluent coming from a nanoLC column into the high-vacuum region of an electron ionization source. In the present research, a nanoLC system was directly coupled to an electron ionization mass spectrometer (EI-MS) without any interface or modification of the ion source. The advantage with respect to atmospheric pressure ionization techniques, normally coupled with LC, is major identification power because of a more extensive and reproducible fragmentation pattern, without any matrix effect or mobile-phase interference. In particular, a nanoLC/EI-MS method was developed for elucidation of the free fatty acid profile in mussel samples, avoiding a previous derivatization step, required when gas chromatographic analysis is involved. A total of 20 fatty acids were reliably identified through the comparison with commercial libraries. A quantitative determination was also carried out by using the response factors approach along with the internal standard method, allowing for quantification of 14 fatty acids. Among them, palmitic acid resulted the most abundant, followed by ω6 arachidonic acid. The quantitative data were compared with those obtained by a well-established technique, such as gas chromatography with flame ionization detection (GC-FID). Both nanoLC/EI-MS and GC-FID methods were validated and similar results were obtained in terms of limit of detection and quantification, resulting in the picomole range, and sensitivity as well was not significantly different, as demonstrated by comparing the slope values of the calibration curves (p < 0.05, from a t-test).