Core-shell structured silica/magnetic nanoparticle composites have recently been subjected to extensive research since the shells could offer protection to the cores and introduce new properties to the hybrid structures, which endue them with great application potentials in various fields. Several approaches have been studied for the synthesis of SiO2 coated on magnetic nanoparticles. These approaches include Stöber process, microemulsion, sodium silicate and tetraethoxysilane hydrolysis, aerosol pyrolysis, layer-by-layer strategy, polymer-templating and sonochemical deposition. This review is focused on describing state-of-the-art synthetic routes and methods for the preparation of silica/magnetic nanoparticle composites. Furthermore, we also introduce main applications of these nanoparticle composites in biomedical scopes and address some challenges in the synthesis of high-quality magnetic nanoparticles.