The theranostic probe based on carbon‐encapsulated iron nanoparticles (CEINs) is presented. First, the conjugates of CEINs and polyethylenimine (PEI) were obtained to modify the surface of CEINs with amino groups. It was archived either by means of direct radical addition of PEI to CEINs (CEINs‐NH‐PEI material) or the amidation‐type reaction between CEINs∼COOH and the polymer (CEINs∼CONH‐PEI material obtained). β‐Cyclodextrin (βCD) was selected as the drug delivery vector. βCD was covalently anchored to the PEI‐functionalized CEINs via the 1,1’‐carbonyldiimidazole‐mediated reaction. The synthesis included the conjugation of folic acid (FA; targeting ligand) to CEINs via the carbodiimide‐mediated amidation‐type process. The innovative method for excluding a side process of the FA@βCD complex formation during the FA conjugation to PEI, was developed. 5‐Fluorouracil (5‐FU) was chosen as the representative drug molecule. 5‐FU was anchored to the CEINs∼PEI∼βCD∼FA nanoplatforms employing the host‐guest chemistry of βCD. The success of the reactions was confirmed by infrared spectroscopy and thermogravimetry. The content of anchored organic compounds depends on the type of linkage between PEI and CEINs. Additionally, 5‐FU release profile was examined at various pH. The highest release of 5‐FU was observed at pH 9.0, whilst the lowest at pH 4.7. This work sheds a new light on application of carbon‐encapsulated iron nanoparticles in nanomedicine as the novel drug delivery theranostic systems.