The transitional millisecond pulsar PSR J1023+0038 is the first millisecond pulsar discovered to emit UV and optical pulses. Here we present the results of the UV and X-ray phase-resolved timing analysis of observations performed with the Hubble Space Telescope, XMM-Newton, and NuSTAR satellites between 2014 and 2021. Ultraviolet pulsations are detected in the high luminosity mode and disappear during low and flaring modes, similar to what is observed in the X-ray band. In the high mode, we find variability in both the UV and X-ray pulse amplitudes. The root mean square pulsed amplitude in the UV band ranges from ~2.1% down to ~0.7%, while it oscillates in the interval 5.5–12% in the X-ray band. As also observed in the optical band, this variability is not correlated with the orbital phase. Notwithstanding the rather low statistics, we have marginal evidence that variations in the pulse amplitude do not occur simultaneously in the UV and X-ray bands. When the UV pulsed amplitude decreases below the detection threshold, no significant variation in the X-ray pulsed amplitude is observed. These oscillations in the pulse amplitude could be caused by small random variations in the mass accretion rate leading to a variation in the size of the intra-binary shock region. Finally, we find that the pulsed flux spectral distribution from the X-ray to the UV band is well fitted using a power-law relation of the form νF_ν^pulsed∼ν^0.4. This supports the hypothesis of a common physical mechanism underlying the X-ray, UV, and optical pulsed emissions in PSR J1023+0038.