Recently, there has been growing interest in fuel cell implementation on aircraft, particularly for Unmanned Aerial Vehicle (UAV) propulsion. The performance of both fuel cell types, cathode air-breathing H-2 Proton Exchange Membrane Fuel Cells (PEMFC/H-2) and passive Direct Methanol Fuel Cells (DMFCs), is dependent on atmospheric conditions such as pressure, relative humidity and temperature. In this study, models at the single-cell level have been used to simulate the corresponding polarization curves on flight conditions, which constitutes a contribution to the use of fuel cells in UAV. After validating these models, several cases of interest relating to UAV operation have been considered, such as cruise flight at different altitudes and horizontal flight when crossing clouds, to compare the performance of both types of fuel cells. Fuel cell temperature has been controlled to avoid high performance degradation. The results show that the effects of atmospheric flight conditions are more important for PEMFC/H-2 than for DMFCs. Low pressure affects PEMFC/H-2 performance to a greater extent than DMFC performance. Atmospheric relative humidity affects PEMFC/H-2 performance, especially at high cell temperatures, whereas DMFC performance is barely affected. Although performance is lost, it is possible to operate fuel cells in UAV propulsion systems at low-medium altitudes. (C) 2018 Elsevier Ltd. All rights reserved.