This paper reports on the manipulation of magnetic nanoparticles between microfluidic channels by the application of an external magnet. Two orthogonal channels were prepared using standard PDMS techniques with pressure-driven flow used to deliver the mobile phase. To study the ability to control magnetic nanoparticles within micrometer-sized channels, Fe2O3, MnFe2O4, and Au nanoparticle samples were compared. For the magnetic particles, transfer between flow streams is greatly increased by placing a permanent magnet beneath the intersection of the channels, but no change is observed for the nonmagnetic Au particles. More nanoparticles are magnetically transferred into the orthogonal channel as the solvent flow rate decreases. We demonstrate the ability to use this technique to perform multiple injections of plugs of magnetic particles by periodic application of a magnetic field.