In this paper, the vibration response analysis of single walled boron nitride nanotubes (SWBNNTs) treated as thin walled tube has been done using finite element method (FEM). The resonant frequencies of fixed-free SWBNNTs have been investigated. The analysis explores the resonant frequency variations as well as the resonant frequency shift of the SWBNNTs caused by the changes in size of BNNTs in terms of length as well as the attached masses. The performance of cantilevered SWBNNT mass sensor is also analyzed based on continuum mechanics approach and compared with the published data of single walled carbon nanotube (SWCNT) for fixed-free configuration as a mass sensor. As a systematic analysis approach, the simulation results based on FEM are compared with the continuum mechanics based analytical approach and are found to be in good agreement. It is also found that the BNNT cantilever biosensor has better response and sensitivity compared to the CNT as a counterpart. Also, the results indicate that the mass sensitivity of cantilevered boron nitride nanotube nanomechanical resonators can reach 10−23 g and the mass sensitivity increases when smaller size nanomechanical resonators are used in mass sensors.