Water and thermal management of an open-cathode proton electrolyte membrane (PEM) fuel cell is developed in this study. A bubble humidifier, which is one of the balance of plant (BOP) systems, is newly installed to control the humidity of the fuel cell. A multiple-input multiple-output (MIMO) fuzzy controller is developed, and proven to be superior in controlling a strong non-linear dynamical fuel cell system in real-time. According to the fuzzy control stratagem, the two main control objectives are the axial fan speed control for regulating temperature and the solenoid valve on/off control of the bubble humidifier for humidity variation. First, the axial fan speed is controlled to keep the fuel cell temperature within the desired point. Second, the bubble humidifier is utilized to humidify the inlet hydrogen to manage the water content of a membrane. After simulating the electrochemical and thermal fuel cell models, the optimal operating conditions are determined. A fuzzy logic controller with five inputs and two outputs is constructed and utilized to regulate the temperature and relative humidity of an open cathode fuel cell in real time. Results show that the proposed fuzzy controller effectively increased the output power of PEM fuel cell. (C) 2017 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.