An aircraft fuel deoxygenation system includes a boost pump, a contactor-separator, and a centrifuge-separator pump. The boost pump is adapted to receive fuel from a fuel source and inert gas from an inert gas source, and is configured to mix the fuel and inert gas and supply a fuel/gas mixture. The contactor-separator is coupled to receive the fuel/gas mixture and is configured to remove oxygen from the fuel and thereby generate and supply deoxygenated fuel with entrained purge gas and separated purge gas. The centrifuge-separator pump is coupled to receive the deoxygenated fuel with entrained purge gas and is configured to separate and remove the entrained purge gas from the deoxygenated fuel and supply the deoxygenated fuel and additional purge gas.