Medical treatment using non-thermal atmospheric pressure plasma (NTAPP) is rapidly gaining recognition. NTAPP is thought to be a new therapeutic method because it could generate highly reactive species in an ambient atmosphere which could be exposed to biological targets (e.g., cells and tissues). If plasma-generated reactive species could stimulate bone regeneration, NTAPP can provide a new treatment opportunity in regenerative medicine. Here, we investigated the impact of NTAPP on bone regeneration using a large bone defect in New Zealand White rabbits and a simple atmospheric pressure plasma (helium microplasma jet). We observed the recovery progress of the large bone defects by X-ray imaging over eight weeks after surgery. The X-ray results showed a clear difference in the occupancy of the new bone of the large bone defect among groups with different plasma treatment times, whereas the new bone occupancy was not substantial in the untreated control group. According to the results of micro-computed tomography analysis at eight weeks, the most successful bone regeneration was achieved using a plasma treatment time of 10 min, wherein the new bone volume was 1.51 times larger than that in the plasma untreated control group. Using H&E and Masson trichrome stains, nucleated cells were uniformly observed, and no inclusion was confirmed, respectively, in the groups of plasma treatment. We concluded the critical large bone defect were filled with new bone. Overall, these results suggest that NTAPP is promising for fracture treatment.