Niobium oxide($Nb_2O_5$) films were deposited on p-type Si wafers at room temperature using in-line pulsed-DC magnetron sputtering system with various frequencies. The different duty ratios were obtained by varying the frequency of pulsed DC power from 100 to 300 kHz at the fixed reverse time of $1.5{mu}s$. From the thickness of the sputtered $NbO_x$ films, it was possible to obtain much higher deposition rate in case of pulsed-DC sputtering than RF sputtering. However, the similar leakage currents and structural characteristics were obtained from the metal-insulator-semiconductor(MIS) structure fabricated with the $NbO_x$ films and the x-ray photoelectron spectroscopy(XPS) results in spite of the different deposition rates. From the experimental results, the $NbO_x$ films sputtered by pulsed-DC sputtering are expected to be used in the fabrication process instead of RF sputtering.