Tilapia (Oreochromis niloticus) is the most cultivated fish species in Brazil. Studies have shown that fish consumption is related to the prevention of cardiovascular diseases due to its high contents of polyunsaturated fatty acids, as omega-3 (n-3) and omega-6 (n-6). In this sense, a new method to determine omega-3 and omega-6 by near-infrared (NIR) spectroscopy and multivariate calibration based on partial least squares (PLS) was proposed. Spectra of fillets of Nile tilapias packed under vacuum were obtained and compared to the reference method (gas chromatography) used for quantification of fatty acids. The outliers were evaluated in the models that were validated by calculation of the parameters for model performance estimation, showing promising results. The appropriate values achieved for accuracy, limits of detection and quantification, indicate that the NIR/PLS models can be an alternative to chromatography in the determination of omega-3 and omega-6 in fillets of Nile tilapia. Furthermore, the spectra acquisition on the vacuum-packed fillet contributes to the NIR/PLS method in terms of cost and quickness.