Carbon nanotubes were successfully functionalized for the first time in a free radical phosphonylation reaction. Three synthetic protocols were proposed. Carbon nanotubes and diethylphosphite reacted in the presence of known radical initiator, such as azobisisobutyronitrile, single electron oxidant—Mn(OAc)3, or under UV radiation. The functionalized material was fully characterized by means of spectroscopic methods, together with microscopic, surface area and thermogravimetric analyses. UV-illumination was found to be the most effective approach for introducing phosphonates onto carbon nanotubes. X-ray photoelectron spectroscopy analysis showed 6% phosphorus in this sample. Moreover, the method was performed at room temperature for only one hour, using diethylphosphite as a reactant and as a solvent. The functionalized carbon nanotubes showed an improved thermal stability, with a decomposition onset temperature increase of more than 130 °C. This makes it very promising material for flame retarding applications.