We present a remanence measurement method using a superconducting quantum interference device (SQUID) to detect trace amount of magnetic nanoparticles (MNPs). Based on this method, a one-dimensional scanning system was established for imaging by utilizing superparamagnetic iron oxide nanoparticles (NPs) as contrast agents. The system was calibrated with 25 nm diameter Fe2O3 NPs, and the sensitivity of the NPs was found to be 10 ng at a distance of 1.7 cm and the spatial resolution was ∼1 cm. A theoretical model of this system was developed and applied to the deconvolution of scanned images of phantoms with two NP injection spots. Using the developed SQUID system, we were able to determine not only the amount and horizontal positions of the injections, but also their depths in the phantoms.