The Late-Miocene Torfufell central volcano (ToCV), situated between the now extinct Snæfellsnes-Húnaflói rift zone and the presently active rift in North Iceland, provides an excellent opportunity to recreate the construction history of a volcanic edifice. We present new U–Pb zircon ages from six silicic units of the ToCV. The results range from 7.15 ± 0.12 to 6.76 ± 0.02 Ma, taken here to represent a ~ 400 kyr time-span for silicic activity at the volcano. Before that, the central volcano had produced basaltic lavas for 600–800 kyr, implying that it was active for ~ 1–1.2 Myr. A stratigraphically documented ~ 1 Myr hiatus above the volcano is contemporaneous with, but shorter than, a major unconformity in the Flateyjarskagi peninsula, considered to result from a major rift relocation in North Iceland. The new U–Pb ages show that silicic volcanism at the ToCV took place 1–2 Myr earlier than assumed previously and nearly synchronously with the rift relocation. As the age progression of the ToCV and the neighboring 5–6 Ma Tinná central volcano conflicts with the generally established geotectonic framework of central N-Iceland, we propose that these two volcanoes were formed at a leaky transform zone that developed to accommodate the rift relocation, with the ToCV formed at its junction with the embryonic rift zone, thus marking the initiation of the presently active rift in North Iceland. Since then, the two volcanoes have drifted away from the rift system due to plate spreading and migration of the plate boundary relative to the Iceland mantle plume.