We report the discovery of one RR Lyrae star in the ultra-faint satellite galaxy Hydra II based on time series photometry in the g, r and i bands obtained with the Dark Energy Camera at Cerro Tololo Inter-American Observatory, Chile. The association of the RR Lyrae star discovered here with Hydra II is clear because is located at 42\prime\prime from the center of the dwarf, well within its half-light radius of 102\prime\prime . The RR Lyrae star has a mean magnitude of i=21.30+/- 0.04 which is too faint to be a field halo star. This magnitude translates to a heliocentric distance of 151 ± 8 kpc for Hydra II; this value is ∼ 13% larger than the estimate from the discovery paper based on the average magnitude of several blue horizontal branch star candidates. The new distance implies a slightly larger half-light radius of {76}-10+12 pc and a brighter absolute magnitude of {M}V=-5.1+/- 0.3, which keeps this object within the realm of the dwarf galaxies. A comparison with other RR Lyrae stars in ultra-faint systems indicates similar pulsational properties among them, which are different to those found among halo field stars and those in the largest of the Milky Way satellites. We also report the discovery of 31 additional short period variables in the field of view (RR Lyrae, SX Phe, eclipsing binaries, and a likely anomalous cepheid) which are likely not related with Hydra II.