Ruthenium dioxide (RuO2) is an important metal widely used in nanoelectronic devices. It plays indispensable roles in applications such as catalysts and supercapacitors. A good understanding of the origin of the flicker or 1/f noise in RuO2 will advance the design and efficiency of these applications. We demonstrate in a series of sputtered RuO2 polycrystalline films that the 1/f noise originates from fluctuating oxygen vacancies which act as dynamical structural defects, i.e., moving scattering centers. Reducing the number of oxygen vacancies by adjusting thermal annealing conditions significantly reduces the noise magnitude γ, the Hooge parameter. We quantify the activation energy distribution function, g(E), and calculate the oxygen vacancy density, nTLS, from the measured γ value. We show that g(E) can be explicitly expressed in terms of γ(T) and the electronic parameters of the metal, where T denotes temperature. The inferred nTLS value is in line with the oxygen content determined from the x-ray photoelectron spectroscopy studies.