During their lifetime, rotating machines experience various problems. Among others, rotor–stator rubbing is one of the most common problems encountered. Therefore, this paper proposes a two-step procedure for rotor–stator partial rub detection. The first step applies the instantaneous angular speed (IAS) measurement. In this paper, the IAS signal is measured at low to moderate sampling rates as an analog signal from the zebra tape encoder. The correction of encoder segment non-uniformity is also briefly presented in the paper. As a means of coping with the nonlinear signal of the partial rub, the variational mode decomposition (VMD) is proposed in the paper, as the second step of the detection procedure. The VMD is a relatively new method with promising results for machinery fault detection. The partial rub detection tool was tested on the laboratory test rig under three different rotor operating conditions; firstly, for constant rotor speed without rubbing, secondly for rotor running at near critical constant speed with light rotor–stator rubbing, and finally under the condition which describes capabilities of the proposed rubbing detection procedure during variable rotor speed operation. The measurements were taken with an optical phase sensor pointed at the zebra tape encoder. The results are presented in the shape of rotor orbits, IAS signals, FFT spectra of IAS signals and VMD spectrograms of IAS signals. It can be concluded that VMD spectrogram of IAS signal yields a clear detection criterion for light partial rotor–stator rubbing by the presence of 1/2×, 3/2× and 5/2× fractional harmonics. Depending on the analyzed conditions of partial rubbing, at least one of the mentioned fractional harmonics should appear.