Ophiolites occur widely in orogenic belts, yet their origins remain controversial. Here we present a modern example with a geodynamic model from Timor, eastern Indonesia, where Earth’s youngest supra-subduction zone (SSZ)-type ophiolitic fragments are exposed. Zircon U-Pb ages and geochemical data indicate a short timespan (~10 to 8 Ma) for the magmatic sequence with boninitic and tholeiitic arc compositions. We interpret the Timor ophiolite as part of the infant Banda arc-forearc complex, which formed with the opening of the North Banda Sea and subsequent arc-continent collision along the irregular Australian continental margin. Our study connects the occurrence of small, short-lived ocean basins in the western Pacific with orogens around the globe where ephemeral SSZ-type ophiolites occur. These orogenic ophiolites do not represent preexisting oceanic crust, but result from upper-plate processes in early orogenesis and thus mark the onset of collision zone magmatism.