A novel and simple method for the preparation of chemically functionalized boron nitride nanotubes (BNNTs) is presented. Thanks to a strong oxidation followed by the silanization of the surface through 3-aminopropyl-triethoxysilane (APTES), BNNTs exposing amino groups on their surface were successfully obtained. The efficacy of the procedure was assessed with EDS and XPS analyses, which demonstrated a successful functionalization of ~15% boron sites. This approach opens interesting perspectives for further modification of BNNTs with several kinds of molecules. Since, in particular, biomedical applications are envisaged, we also demonstrated in vitro biocompatibility and cellular up-take of the functionalized BNNTs.