Semen stain is one of the most important biological evidence at sexual crime scenes. Age estimation of human semen stains plays an important role in forensic work, and it is rarely studied due to lack of well-established methods. In this study, the technique called attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) coupled with advanced chemometric methods was employed to determine the age of semen stains on three different substrates: glass slides, tissues and fabric made of regenerated cellulose fibres up to 6 d. Partial least squares regression (PLSR) was used in conjunction with spectral analysis for age estimation, and the results generated high R 2 values (cross-validation: 0.81, external validation: 0.74) but a narrow margin of error for root mean square error (RMSE) (RMSE of cross-validation: 0.77 d, RMSE of prediction: 1.02 d). Additionally, our results indicated the robustness of PLSR model was not weaken by the influence of different substrates in this study. Our results indicate that ATR-FTIR, combined with chemometric methods, shows great potential as a convenient and efficient tool for age estimation of semen stains. Moreover, the method could be applied to routine forensic investigations in the future.