A linear array of Nd-Fe-B magnets has been designed and constructed in an inverted Halbach configuration for use in separating magnetic nanoparticles. The array provides a large region of relatively low magnetic field, yet high magnetic field gradient in agreement with finite element modeling calculations. The magnet assembly has been combined with a flow channel for magnetic nanoparticle suspensions, such that for an appropriate distance away from the assembly, nanoparticles of higher moment aggregate and accumulate against the channel wall, with lower moment nanoparticles flowing unaffected. The device is demonstrated for iron oxide nanoparticles with diameters of ~ 5 and 20 nm. In comparison to other approaches, the inverted Halbach array is more amenable to modeling and to scaling up to preparative quantities of particles.