Late arterial thrombosis of a free flap is rare and usually unsalvageable because it is hard to detect. We herein report 2 cases of arterial thrombosis of a free flap after microvascular head and neck reconstruction due to the combined factors of pedicle artery loop and compression by a swollen submandibular gland, the occurrence of thrombosis in both of which was > 72 hours after the operation. In case 1, the arterial thrombosis was undetectable, and it was too late for a successful take-back operation, so the flap was lost. However, we applied the lessons learned from case 1 and were able to detect the late arterial thrombosis of case 2 at an early stage; we subsequently salvaged the flap successfully. During the take-back operation in both cases, it was found that the submandibular gland became swollen and compressed the pedicle artery, which then became occluded due to a steep loop formation. Postoperative swelling of the submandibular gland can sometimes compress the vascular pedicle, and complete occlusion of the pedicle artery may occur when it is looped. Meticulous care concerning the geometry of the vascular pedicle is required to avoid such complications.