A carbon dioxide separation system for a fuel cell system having a small volume and weight of a separation device and of a membrane, at simultaneous increase of the separated volume of carbon dioxide, comprises a separation device for containing a fluid phase, a carbon dioxide phase, and a two phase fluid including fluid and carbon dioxide. The separation device comprises a two phase fluid inlet, a fluid outlet, a carbon dioxide outlet, a carbon dioxide separation membrane, and a flow restrictor creating a backpressure which presses separated carbon dioxide through the carbon dioxide separation membrane. The flow restrictor comprises at least one narrow aperture, and is mounted downstream of the separation device. The carbon dioxide separation membrane is positioned in the separation device in such a manner that at least a part of the total membrane area is arranged above a two phase fluid level and is in touch with carbon dioxide contained in the separation device above the two phase fluid level.