Stephan’s Quintet (SQ, co-moving radial distance = 85 ± 6 Mpc, taken from the NASA/IPAC Extragalactic Database (NED)1) is unique among compact groups of galaxies2–12. Observations have previously shown that interactions between multiple members, including a high-speed intruder galaxy currently colliding into the intragroup medium, have probably generated tidal debris in the form of multiple gaseous and stellar filaments6,8,13, the formation of tidal dwarfs7,14,15 and intragroup-medium starbursts16, as well as widespread intergalactic shocked gas5,10,11,17. The details and timing of the interactions and collisions remain poorly understood because of their multiple nature18,19. Here we report atomic hydrogen (H i) observations in the vicinity of SQ with a smoothed sensitivity of 1σ = 4.2 × 1016 cm−2 per channel (velocity bin-width Δv = 20 km s−1; angular resolution = 4′), which are about two orders of magnitude deeper than previous observations8,13,20,21. The data show a large H i structure (with linear scale of around 0.6 Mpc) encompassing an extended source of size approximately 0.4 Mpc associated with the debris field and a curved diffuse feature of length around 0.5 Mpc attached to the south edge of the extended source. The diffuse feature was probably produced by tidal interactions in early stages of the formation of SQ (>1 Gyr ago), although it is not clear how the low-density H i gas (NH i ≲ 1018 cm−2) can survive the ionization by the intergalactic ultraviolet background on such a long time scale. Our observations require a rethinking of properties of gas in outer parts of galaxy groups and demand complex modelling of different phases of the intragroup medium in simulations of group formation.