A methodology based on Fourier transform infrared (FTIR) spectroscopy with different absorption modes, combined with chemometrics techniques, was developed as a tool to quantify the free fatty acids (FFAs) in extra virgin olive oils (EVOOs). The range of FFA contents of calibration samples was extended by adding 0–1.00% oleic acid to refined and deodorized olive oil (RDOO) containing 0.00% FFA. Calibration models were implemented using the partial least-squares (PLS) regression technique. Two absorption modes, reflection and transmission, and two pretreatments, normal and first derivative spectra, were tested in several infrared spectral regions. In order to construct the calibration models, 15 calibration samples were scanned in different absorption modes, and 10 different brands of EVOOs were used for checking the predictive capacity of the best calibration model. The results showed that the best predictions were achieved using normal spectra in the transmission mode using 100 µm CaF2 flow cell with the highest correlation coefficient (R2) of 0.99979 and the lowest root mean square error of calibration (RMSEC) of 0.00441 and root mean square error of cross-validation (RMSECV) of 0.0107 in the infrared spectral region 1724–1646 + 3324–3023 cm−1. The method developed is fast, environment-friendly, and it could be easily used in olive oil industries for the rapid and reliable quantification of FFA content in EVOOs.