The life cycle human health (HH) impacts related to aviation biofuels have been understood in a limited way. Life cycle impact assessment (LCIA) methods for assessing HH are often associated with a high level of uncertainty and a low level of consensus. As a result, it remains challenging to perform a robust assessment of HH impacts with a suitable LCIA method. This study aims to systematically compare six commonly used LCIA methods for quantifying HH impacts, in order to empirically understand the potential impacts of aviation biofuel production on HH and how the results are affected by the choice of methods. Three aviation biofuel production pathways based on different feedstocks (sugarcane, eucalyptus, and macauba) were analyzed and compared to fossil aviation biofuels, on the basis of a functional unit of 1 MJ aviation fuel. The majority of the LCIA methods suggest that, in respect to midpoint impacts, macauba-based biofuel is associated with the lowest impacts and eucalyptus-based biofuel the highest; whereas at endpoint level, the results are more scattered. The LCIA methods agree that biomass conversion into aviation biofuel, H2 production, and feedstock cultivation are major contributors to life cycle HH impacts. Additionally, we provide a guideline for determining an appropriate method for assessing HH impacts.