Abstarct: Abstract In order to improve the treatment of cancer and more effect of anti-cancer drugs such as dosage control and reduction of damage to healthy tissues of body, targeted drug delivery and release is of great importance. In the past decade, the nanotubes was introduced as a good candidate for drug delivery systems. Among the nanotubes family, boron nitride nanotubes (BNNTs) due to non-toxicity, biocompatibility and solubility in water have received more attention. Therefore, in the present work, the encapsulation behavior of the gemcitabine anti-cancer drug into the edge decorated boron nitride nanotubes with the hydroxyl functional groups in aqueous solution was investigated using molecular dynamics simulation. The results of interaction energy, hydrogen bonding and mean square displacement showed that the gemcitabine encapsulates faster into the functionalized BNNT than the natural BNNT, and the tendency of the drug to move back and forth along the nanotube. Also, the releasing of gemcitabine was studied from functionalized BNNT using fullerenes molecules. Similar to natural BNNTs, the presence of hydroxyl functional group on the edge of nanotube was no effect on the release process of drug. Therefore, the fullerene molecule is not a suitable release agent for the gemcitabine anti-cancer drug in functionalized BNNT.