We have performed a density functional theory study to investigate the effect of carbon doping on Stone–Wales (SW) defective sites in the armchair (4, 4), (5, 5) and (6, 6) BNNTs, in order to remove structural instability induced by homonuclear N–N and B–B bonds. Two different orientations of SW defect are considered, parallel and diagonal, and then C atoms are doped at different positions of the defect sites. In general, it seems that among the considered arrangements, C atoms prefer to be substituted for the homonuclear B–B bond. The larger HOMO–LUMO band gaps for the most stable configurations indicate that C doping at B–B sites is kinetically more favorable than the other ones. According to calculated nuclear quadrupole resonance (NQR) parameters as a result of C-doping on SW defective sites, the quadrupole coupling constants (CQ) of boron nuclei at defective sites decrease by about 0.508–1.406 MHz while 14N CQ of the defective sites, except for N8, increases. Interestingly, CQ of the N sites directly connected to dopant sites has maximum increment (0.612–2.596 MHz) while CQ of the N sites belonging to the B2N3 pentagon is undergone to some minor changes.