Diurnal very low frequency subionospheric radio wave phase measurements show a night-to-day transition pattern. During this sunrise transition a phase perturbation, which consist of a phase overshoot followed by a small phase recovery to normal daytime values, is often observed. The variability of the size of this sunrise phase perturbation and its maximum and end times were monitored to identify the associated physical causes. Very low frequency signal from the 22.1-kHz UK transmitter (call sign GVT) recorded at Sodankylä, Finland, from 20 April 2010 to 31 December 2016 were used. The timing at the maximum of the phase perturbation period has an annual pattern that is well described by the seasonal variation of the sunrise time 28 km above the transmitter. Variations in ozone number density at 38–42-km altitudes are better correlated (R = 0.7) with the sunrise phase perturbation variability than at any other altitudes below ~80 km, and exhibit higher correlation values than for atmospheric temperature. Our results show that the main characteristics of the observed very low frequency sunrise phase perturbation arise from shadowing of short-wavelength solar UV flux from the D region ionosphere due to stratospheric ozone absorption.