Abstract The short-time Fourier transform (STFT) based instantaneous frequency (IF) estimator has been used for polynomial phase signal (PPS) parameters estimation. This estimator is biased but it is less sensitive to the noise influence than the higher-order techniques such as the high-order ambiguity function (HAF). Here, we have developed a method for estimation of the optimal window width in the STFT for the PPS estimation. Obtained results are then refined with the strategy proposed recently by O'Shea. In this way the resulting estimates of parameters outperform the HAF based ones.