Abstract The spin-one honeycomb bilayer XY antiferromagnet has been studied taking into account the effect of the next-near neighbor J2 exchange interactions and single-ion easy plane anisotropy, using a flavor wave theory. We found that, at a critical point α C = 13.8 , where α = J ⊥ / J 1 is the ratio between the interlayer J ⊥ to the intralayer near neighbor J1 exchange interaction, the system shows a quantum phase transition from an Neel ordered phase to a paramagnetic phase. The phase diagram at zero temperature is presented.