The only place where Neogene–Quaternary rocks crop out for the entire Tuscan Archipelago in the Northern Tyrrhenian Sea is the island of Pianosa. In particular, the Miocene deposits record the depositional and tectonic evolution of the Northern Tyrrhenian region during this time period. These deposits are subdivided into two successions separated by a low-angle unconformity. The older, middle Burdigalian succession represents a calciturbidite shallow marine system, whereas the younger late Tortonian–early Messinian succession comprises a continental alluvial system that evolves upwards into a lagoonal–marginal marine environment. Here we present sedimentological, palaeontological and petrographical data that support a new stratigraphic and palaeogeographical framework for reconstructing the opening of the Northern Tyrrhenian back-arc basin. The early Miocene succession records a pre-rift marine depositional phase followed by a late Burdigalian–Langhian erosional phase. This was followed by a period of synrift continental-marginal deposition, as recorded by the late Miocene succession, terminated by an important phase of uplift, probably induced by the start of magmatic activity in the Tuscan Archipelago area.