We report an application of a simultaneous perturbation stochastic approximation (SPSA) algorithm to filtering systematic noise (SN) with non-zero mean value in photoemission data. In our analysis we have used a series of 50 single-scan photoemission spectra of W(110) surface where randomly chosen SN was added. It was found that the SPSA-evaluated spectrum is in good agreement with the spectrum measured without SN. On the basis of our results a wide application of SPSA for evaluation of experimental data is anticipated.