It is well-known that defect healing in boron nitride nanotube (BNNT) is a helpful procedure for their potential applications in different devices. In this work, the adsorption of a single CO molecule on the B- and N-vacancy defective BNNTs is studied by means of density functional theory calculations. The healing process proceeds via three main steps: (1) the physisorption or chemisorption of CO molecule over the vacancy site; (2) the combination of C atom of the CO molecule with three N or B atoms around the defective site and (3) the removal of extra atomic O from C-doped BNNT by another CO molecule. Thus, C-doped BNNT is formed without introducing additional defects. The proposed mechanism is not only theoretically possible, but also due to the low energy barrier, the doping process can be easily achieved at room temperature. Our research can be useful in purification of BNNTs and also in the removal of toxic CO gas.