Background: The purpose of using nano-carriers for drugs delivery, such as nanotubes, is slow release of drug and reducing side effects of drugs. Drugs are very active due to their many functional groups. Therefore, reactivity of drug is reduced by being in nanotube field due to electronic resonance of drug with nanotube and it stays longer in body. As a result, less amount of drug is used and fewer side effects occur. Materials and methods: In present study, boron nitride nanotubes (n = 9, m = 9) with 7 angstroms length and carbon nanotubes (n=9, m=9) with 7 angstroms were used to compare effects of encapsulating anticancer drug Floxuridine with this nanotube. Using density functional theory (DFT) at theoretical level of B3LYP / 6-31G *, structure of drug and BNNT (9, 9-7), CNT (9, 9-7) and nano-drug systems were optimized. Results: Using optimized structures, spatial parameters such as bond length and bond angels, HOMOLUMO orbitals, graphs of density of states (DOS), natural bond orbital (NBO), electronic properties, parameters of atoms in molecules (AIM) and molecular electrostatic potential (MEP) were discussed. Conclusion: Analysis of adsorption energy and thermodynamic functions shows that the process of encapsulation of the drug by both nanotubes is favorable and based on the results of NBO and AIM, BNNT nanotubes are more suitable for encapsulation of fluoxoridine.