A variety of cells can be applied as vectors for the targeted delivery of chemotherapeutic or gene therapeutic agents to neoplasms. Macrophages are regarded as promising candidates for cell-based therapy. Accurate assessments of the efficacy and safety profiles of cell-based therapy products require the collection of data on their biodistribution and fate. The study of living cell distribution in vivo necessitates the utilization of a combination of methodologies to obtain more precise data regarding the fate of cells after their administration into animals. In the present study, a murine RAW 264.7 cell line was engineered to express enhanced green fluorescent protein (GFP). These cells were labeled with 50 nm magnetic nanoparticles (MNPs) for non-invasive real-time monitoring in mice using the magnetic particle quantification (MPQ) technique. The combination of high sensitivity and multimodality of the approach used permitted the acquisition of comprehensive data on the biodistribution of RAW-GFP cells in mice. For the first time, non-invasive, real-time monitoring of the dynamics of MNP-loaded macrophages in the bloodstream of mice has been achieved via the MPQ technique. Following intravenous administration, the cells are rapidly eliminated from the bloodstream, with subsequent accumulation mainly in the lungs and the liver. This may impose limitations on the use of such cells for drug delivery to other regions of a living organism.