Hybrid nanostructured materials have been broadly studied in the last years. Boron nitride nanotubes (BNNTs) have chemical and thermal stability, in addition to its excellent mechanical properties. Furthermore, the fluorescence presented by these BNNTs can be useful for many applications. On the other hand, Poly-ε-caprolactone (PCL) is a widely used polymer in biomedical and pharmaceutical applications. PCL is biocompatible and may be degraded by hydrolytic and enzymatic reactions without toxicity. Hence, PCL nanofibers, produced by electrospinning, can be applied as scaffolds for tissue engineering. In this study, boron nitride nanotubes (BNNTs) were incorporated in the matrix of PCL nanofibers through electrospinning process. This hybrid nanomaterial was systematic characterized through thermogravimetry analysis, Fourier transformation infrared spectroscopy (FTIR) and the morphological characteristics were available by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Furthermore, the biological experiments showed that the hybrid nanomaterial is biocompatible, and allows cell adhesion. From the obtained results it was possible to confirm that this hybrid system has the desired features for application as biosensor and tissue engineering