This paper presents a control solution based on dynamic disturbance decoupling control (DDC) for a centrifugal compression system, which is used to supply the compressed air to the fuel cell, thereby reacting with the hydrogen to produce electricity. As a result of its ultra-high speed, this compressor has a great advantage of ultra-compactness, which makes it more suitable for transportation applications. However, unlike positive displacement compressors, the centrifugal compressor has strong coupling between mass flow and pressure, which gives rise to the difficulty of control and also limits its operating region. In this paper, a unique dynamic DDC strategy, based on the active disturbance rejection control (ADRC) framework, is developed to control the mass flow and pressure simultaneously. The experimental results show that, compared with a traditional PI controller this controller performs better in both the transient and steady states. This control system has been validated on a 10 kW fuel cell model under load variations. Copyright (C) 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.