A new method is presented for quantitative determination of naltrexone in aqueous solutions based up on the wavelength selection in mid-FTIR spectra using partial least squares (PLS) technique. The main aim is to find wavelengths which produce significant improvements in PLS prediction. PLS wavelength selection treatment is performed on the data obtained by attenuated total reflectance Fourier transform infrared spectrometry in 830–1800 cm−1 wavenumber range. No separation or extraction steps are required prior to determination procedure and a simple pretreatment is performed. Absorbance spectra were employed for measurements using a set of 7 aqueous standard solutions of naltrexone. The method is applicable for pharmaceutical samples in aqueous solution in the presence of impurities, while it is simple, rapid and accurate. The results obtained from real samples were compared with those obtained using Ultra Violet spectrophotometry as a reference method. Statistical parameters such as R2, REP, RMSEC and RMSECV were evaluated, and number of factors, number of scans and resolution were also optimized. In this method R2 and RMSEC for proposed procedure have been found to be 0.9983 and 0.1297, respectively.