Head and neck reconstruction is complicated and is made even more challenging by free flap failure. We identified risk factors associated with free flap failure in records extracted from a nationwide database of a 23 million populations. We used International Classification of Diseases, Ninth Version, codes 140 to 149 and 161 to identify patients in Taiwan's National Health Insurance Research Database with head and neck cancer between 2000 and 2013. Patient's age, sex, neoadjuvant treatment, comorbidities, and anticoagulation use were also retrieved. Free flap reconstruction twice, or free flap and pedicle flap reconstructions during the same hospitalization were recorded as free flap failure. Logistic regression was used to identify factors that increased risk of free flap failure. A total of 21,548 patients with head and neck cancer were identified; 883 (4.1%) experienced free flap failure. Use of aspirin, clopidogrel, urokinase, prostaglandin (PGE1), low-molecular-weight heparin, and operation time were associated with free flap failure. However, some potential confounders could not be identified from the database. Several statistically significant findings were prone to influence by potential confounders. The clinically applicable result was that longer operation time and preoperative chemotherapy could increase the likelihood of free flap failure. On the other hand, several factors were proved to be irrelevant to free flap failure.