Head and neck patients undergoing microvascular reconstruction are at high risk for thromboembolism. While the prevention of thromboembolism has become an essential aspect of care, within the field of microsurgery, concern for anastomotic complications have hindered the creation of an accepted regimen. The aim of this review was to evaluate the risks and benefits of prophylactic agents for thromboprophylaxis. A literature search was conducted in MEDLINE, Cochrane Library, and PubMed/NCBI databases. Articles discussing thromboprophylaxis in otolaryngology, head and neck surgery, or microvascular reconstruction were considered in the review from the past 30 years. The majority of patients undergoing microvascular surgery have multiple risk factors for thrombus formation. Several consensus guidelines exist for the prophylaxis in patients who are critically ill, undergoing surgery, or with malignancy. Significant evidence supports the routine use of mechanical means, such as early mobilization and pneumatic compression along with subcutaneous heparin. Low-molecular-weight heparin is also frequently utilized, although results are largely divided. Data on aspirin remain equivocal. Studies on microvascular failure and flap loss have demonstrated little to no association with chemoprophylaxis. The evidence for postoperative thromboprophylaxis regimens in patients undergoing head and neck free tissue transfer is variable. Multiple studies have supported the use of unfractionated heparin or low-molecular-weight heparin. There appears to be an expert consensus for the combined use of mechanical prophylactic methods and chemical prophylaxis. Prospective randomized trials are required to validate the most effective combination of chemoprophylaxis agents.