Nowadays, attempts to use nanoparticles for medical applications are on the rise. However, the effect of nanoparticles in the body has not been clarified. In this study, we aimed to examine the pharmacokinetics of magnetized nanoparticles. FITC conjugated SA-MnMEIO nanoparticles were prepared for the purpose of tracing. Nanoparticles (15 nm diameter) were injected into the tail vein of BALB/c mice at a dose of 20 mg (Mn+Fe)/kg. A mouse was housed in a metabolic cage and sacrificed serially up to 14 days for the sampling of blood and tissues from various organs (i.e., heart, kidney, liver, and spleen). The concentration of nanoparticles was measured by detecting FITC using spectrofluorophotometer. Nanoparticles showed a half-life of 8.20 h. The fluorescence intensities of nanoparticles in tissues showed different time-dependent patterns among different organs. In the heart and the liver, the fluorescence intensities increased up to 2 weeks of observation, while those in the kidney and the spleen decreased. The results indicate that nanoparticles have unique pharmacokinetic characteristics and suggest that pharmacokinetic study is essential for the development of new nanoparticles for medical use.