A fluid dynamics simulation was used to study the effect of the internal movement of hydrogen bubbles on current efficiency in a pilot scale fluorine electrolyser. Two dimensional modelling of the gas-liquid free convection was carried out using the Estet-Astrid (EA) finite volume code. The effect of hydrodynamics is well highlighted and calculations show that a significant fraction of the hydrogen bubbles can migrate, under certain conditions, into the fluorine compartment. This fraction of hydrogen recombines with fluorine and thus decreases the Faradaic current efficiency of the electrolyser. The numerical results confirm the experimental trends observed on the pilot. The model also clarifies the effect of hydrogen bubble diameter on Faradaic current efficiency.