Aims: We aim at constraining evolutionary models at low mass and young ages by identifying interesting transiting system members of the nearest OB association to the Sun, Upper Scorpius (USco), which has been targeted by the Kepler mission. Methods: We produced light curves for M-dwarf members of the USco region that has been surveyed during the second campaign of the Kepler K2 mission. We identified by eye a transiting system, USco J161630.68-251220.1 (=EPIC 203710387) with a combined spectral type of M5.25, whose photometric, astrometric, and spectroscopic properties makes it a member of USco. We conducted an extensive photometric and spectroscopic follow-up of this transiting system with a suite of telescopes and instruments to characterise the properties of each component of the system. Results: We calculated a transit duration of about 2.42 h that occurs every 2.88 days with a slight difference in transit depth and phase between the two components. We estimated a mass ratio of 0.922 ± 0.015 from the semi-amplitudes of the radial velocity curves for each component. We derived masses of 0.091 ± 0.005M⊙ and 0.084 ± 0.004M⊙, radii of 0.388 ± 0.008R⊙ and 0.380 ± 0.008R⊙, luminosities of log (L/L⊙) = -2.020-0.121+0.099 dex and -2.032-0.121+0.099 dex, and effective temperatures of 2901-172+199 K and 2908-172+199 K for the primary and secondary, respectively. Conclusions: We present a complete photometric and radial velocity characterisation of the least massive double-line eclipsing binary system in the young USco association with two components close to the stellar/substellar limit. This system falls in a gap between the least massive eclipsing binaries in the low-mass and substellar regimes at young ages and represents an important addition to constraining evolutionary models at young ages. Based on observations made with telescopes (GTC, WHT) installed in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias, in the island of La Palma.