Boron nitride nanotubes (BNNTs) are excellent nanofillers to enhance the mechanical and thermal properties of polymer nanocomposites. Despite the rapid progress in the effective syntheses of BNNTs, the ease of processability and solubility are major roadblocks for their widespread applications. The present work reports for the first time: a facile and environment-friendly green approach for aqueous bioinspired functionalization of boron nitride nanotubes through the use of dopamine, a synthetic mimic of mussel adhesive proteins. This approach is based on the affinity of the amino group of dopamine molecules for the boron atoms in BNNTs and π–π interactions as well as van der Waals interactions between the BNNTs network and dopamine molecules. Functionalization of the boron nitride nanotubes was evidently found to be associated with the existing π–π bonding and van der Waals interactions at the BNNT surfaces, involving the aromatic core structures of the dopamine molecules based on various characterizations. The resultant functionalized BNNTs are highly dispersible in water and a number of solvents. Polymer nanocomposites were prepared using pristine and dopamine functionalized BNNTs as reinforcement in a poly(vinyl difluoroethylene) matrix and tested for the thermal and mechanical properties. The functionalized BNNT reinforced polymer nanocomposites exhibit superior properties as compared to nanocomposites based on pristine BNNTs. This comprehensive study indicates that dopamine functionalized BNNTs are promising materials for various applications and are expected to form the basis of a new class of chemically reactive nanostructures.