We report on paleomagnetic directions gathered from 33 sites from (mostly Holocene) volcanics from Stromboli, loosely dated at present by few K/Ar and ¹⁴C ages. In order to provide dating, the paleomagnetic directions were compared to the Holocene paleosecular variation of the geomagnetic field for the Mediterranean region, derived from direct geomagnetic observations and several archeomagnetic-paleomagnetic data sets. Petrochemical analyses from the paleomagnetic specimens revealed that each Holocene eruptive cycle of Stromboli was characterized by peculiar chemical characteristics. We suggest that before the 20th century AD paroxysms, powerful spatter-forming eruption(s) occurred during the 17th century AD, followed by three centuries of less energetic eruptions, when spattering was limited to the summit cones. A robust data set (4 sites, 52 samples) from the S. Bartolo flow, partially buried below the Stromboli village, constrains its age to 360 BC to 7 AD, in Greek-Roman times. The ca. 6200 years BP age inferred for a scoria exposed below a characteristic pyroclastic succession suggests its correlation with the Secche di Lazzaro pyroclastics, a major phreatomagmatic eruption occurring during the 6th millennium BP, synchronous with the major volcanotectonic collapse of the Sciara del Fuoco. Ages were provided for many lavas from the Neostromboli sequence (including the Labronzo, Nel Cannestrà, and Ginostra flows), indicating that huge effusive activity from lateral fissures fed by an evolving magma chamber occurred in the ∼6200–8000 years BP time window. The absence of volcanics with ages comprised between the 6th millennium BP and 400 BC implies a puzzling three-millennia “eruption gap” at Stromboli.