This study was designed to compare the outcome and analyze the operation-related risk factors in free flap reconstruction for patients with primary and recurrent head and neck cancers. A 1:1 propensity score-matched analysis of the microsurgery registry database of the hospital. The primary outcome of the free flap reconstruction had a higher failure rate in the recurrent group than the primary group (5.1% vs. 3.1%, p = 0.037). Among the 345 pairs in the matched study population, there were no significant differences between the primary and recurrent groups regarding the rate of total flap loss (3.5% vs. 5.5%, p = 0.27) and secondary outcomes. This study revealed that free flap reconstruction had a higher failure rate in the recurrent group than the primary group, but such a difference may be attributed by the different patient characteristics.