Liquid–liquid extraction of metal ions was carried out in a microfluidic device which had intermittent partition walls in the center of the confluent microchannel 100 µm wide, 20 µm deep and 3 cm long. The intermittent partition walls (50 µm long) stabilized a two-phase (n-heptane–water) flow and allowed clear phase separation at the end-junction of the microchannel. Using this two-phase flow in the microchannel, yttrium ions were successfully extracted in a complex form with an extractant PC-88A (2-ethylhexyl phosphonic acid mono-2-ethylhexyl ester) from a feed aqueous phase to a n-heptane phase within a contact time of 1.5 s. Although the apparent interfacial area in the microchannel was reduced by introducing the partition walls, the presence of the partition walls improved the extraction efficiency 2–3 fold at a contact time of 0.12–0.24 s. Flow analyses using fluorescent beads and a computational fluidic dynamics simulation revealed that the partition walls induced a slight turbulence in the two-phase flow in the microchannel. This slight turbulence would result in the mixing of the aqueous phase and promote the transport of yttrium ions from the aqueous feed phase to the organic extractant phase.