A pulsed reactive magnetron sputtering system with a tungsten target and a gas mixture of argon and oxygen was investigated as a source for the deposition of semiconductor WO3 thin films on soda lime glass substrates and on the glass with transparent conductive SnO2:F (FTO) electrode. The reactive sputtering process was performed in HiPIMS mode with low pulse repetition frequency fp ≈ 50–100 Hz and short pulse duration in HiPIMS discharge Ton = 100 μs. The second mode investigated was the mid-frequency (MF) magnetron discharge with pulse frequency fp = 40 kHz and pulse length Ton = 15 μs. The plasma parameters were investigated for both HiPIMS and MF modes using the planar RF probe operating at the frequency fprobe = 350 kHz and the grid QCM with biased collector electrode. Ion density ni and tail electron temperature (Te) were determined in both pulsed reactive magnetron sputtering discharge modes with time resolution. The maximum value ni ≈ 5 · 1017 m−3 was found in the reactive HiPIMS mode, and the maximum value ni ≈ 7 · 1016 m−3 was found in the reactive MF (40 kHz) mode. The degree of ionization of sputtered particles in reactive HiPIMS was determined for different values of (QO2) and was found to be in the range of ri ≈ 0.1–0.3. The deposition rate determined by QCM in reactive HiPIMS was practically independent on (QO2), but in the case of reactive MF, the measured deposition rate decreased significantly with increasing (QO2). The WO3 films deposited in both modes have a predominantly monoclinic crystal structure. The light and dark conductivity and the light/dark conductivity ratio (Ld) were measured under dark conditions and UV light illumination. At higher (QO2), the maximum value of Ld ≈ 300 was found for MF deposited WO3 and the maximum value of Ld ≈ 30 was found for HiPIMS deposited WO3. The photoelectrochemical measurement of WO3 deposited on FTO electrodes confirmed the n-type conductivity, and these films functioned as photoanodes in photoelectrochemical cells. MF deposited WO3 films systematically exhibited slightly higher photocurrents than HiPIMS deposited WO3. It was shown that these optimum photocurrents for HiPIMS and MF were found at QO2 ≈ 80 sccm and could not be improved by further increasing of (QO2).