Omega-3 long-chain polyunsaturated fatty acids (n-3 LCPUFA) have several health benefits. In particular, low n-3 LCPUFA status is associated with cardiovascular disease (CVD) and led to the development of the omega-3 index that is the proportion of eicosapentaenoic acid and docosahexaenoic acid in the erythrocyte membranes, as a marker of CVD risk. Most methods used to measure the omega-3 index are laborious and time consuming. Therefore, the aim of this study was to develop a high-throughput method for the extraction and measurement of erythrocyte fatty acids and the omega-3 index. For sample extraction and quantification, two methods were used; a single-step extraction, degradation, and derivatization method by Lepage and Roy, followed by gas chromatography flame ionization detection (GC-FID), which is commonly used and a high-throughput method using an automated methyl tert-butyl ether extraction followed by electrospray ionization mass spectrometry. Both methods were first applied to the analysis of known concentrations of synthetic phospholipid (PL) mixtures to determine recovery and precision prior to their application in the analysis of human erythrocytes. The range of recoveries over five synthetic PL mixtures were 86.4–108.9% and the coefficient of variation was <10% (within-run) and ≤15.2% (between-run). Both methods showed high correlation (R = 0.993) for the omega-3 index and there was no systematic bias in the detection of omega-3 index using either method. The new high-throughput method described here offers considerable advantages in terms of simplicity and throughput compared to the GC-FID method and provides additional information on molecular PL concentrations.