Ferrofluids or magnetic nanofluids are highly stable colloidal suspensions of magnetic nanoparticles (NPs) dispersed into various base fluids. These stable ferrofluids possess high thermal conductivity, improved thermo-physical properties, higher colloidal stability, good magnetic properties, and biocompatibility, which are the primary driving forces behind their excellent performance, and thus enable them to be used for a wide range of practical applications. The most studied and advanced ferrofluids are based on iron oxide nanostructures especially NPs, because of their easy and large-scale synthesis at low costs. Although in the last decade, several review articles are available on ferrofluids but mainly focused on preparations, properties, and a specific application. Hence, a collective and comprehensive review article on the recent progress of iron oxide nanostructures based ferrofluids for advanced biomedical applications is undeniably required. In this review, the state of the art of biomedical applications is presented and critically analyzed with a special focus on hyperthermia, drug delivery/ nanomedicine, magnetic resonance imaging, and magnetic separation of cells. This review article provides up-to-date information related to the technological advancements and emerging trends in iron oxide nanostructures based ferrofluids research focused on advanced biomedical applications. Finally, conclusions and outlook of iron oxide nanostructures based ferrofluids research for biomedical applications are presented.