XMMU J134736.6+173403 is an X-ray source discovered serendipitously by XMM-Newton, which was found to be spatially coincident with a pair of galaxies, including a Seyfert 2 galaxy, but presented in 2003 a very sharp persistent flux drop of a factor of 6.5 within 1 h. From the analysis of a set of 29 Swift observations conducted from 2008 February 6 to 2008 May 23, we discovered twin-peak quasi-periodic oscillations (QPOs) with periods of 23.82 ± 0.07 h and 71.44 ± 0.57 h. Using a Chandra observation of 2008, we evaluate more accurately the position of the X-ray source and show that the new source coordinates coincide with the position of the Seyfert 2 galaxy. We provide a detailed spectral energy distribution (SED) of the active galactic nucleus (AGN) counterpart using multiwavelength observations. The AGN is radio-loud and the broad-band SED modelling indicates a black hole with a mass of 9.8 x 106 M☉, which accretes at an Eddington ratio of 0.047. QPOs for active galaxies have been reported so far in only few cases, the most reliable one being from RE J1034+396 for which a 1 h periodicity has been discovered analysing a 91 ks XMM-Newton observation. Twin-peak QPOs with an observed frequency ratio of 3:1 have not been reported so far for any AGN. From resonance models of the epicyclic frequencies, we evaluate the different possible mass-spin relations. It's still not clear what could have been the origin of the high flux and sharp drop only observed in 2003.