The mouse model of intraluminal suture middle cerebral artery occlusion (MCAO) is still associated with several issues, such as variability of infarction volume and survival. Thus, the method is far from standardization. The effect of blood flow in the pterygopalatine artery (PPA) in the mouse MCAO model remains obscure. While producing mouse MCAO models using commercially available silicone-coated monofilaments, we temporarily occluded the common carotid artery (CCA) or PPA to determine whether cerebral blood flow (CBF) values, infarct size and the stability of the model would be affected. Forty male C57BL/6 mice were divided into 3 groups: MCAO with blocked CCA blood flow (MCAO-C; n=12), MCAO with blocked PPA blood flow (MCAO-P; n=16) and MCAO without either CCA or PPA blood flow blockage (MCAO-U; n=12). We found that the CBF values were significantly higher during occlusion in the MCAO-U than in the other two groups (p<0.001). We stained whole brains from each group at 24h after reperfusion with 2% 2,3,5-triphenyltetrazolium chloride. Although mean infarct volume did not obviously differ between the MCAO-U and other two groups, infarct volumes varied significantly more within the MCAO-U, than in the other two groups (p<0.05). We concluded that collateral circulation from the PPA to the brain significantly influences the MCAO model, and cannot be ignored. An approximately consistent mouse MCAO model can be generated using commercially available silicone-coated sutures while blocking PPA blood flow during occlusion.