Labyrinth seals are commonly used in turbomachinery in order to control leakage flows. Flutter is one of the most dangerous potential issues for them, leading to High Cycle Fatigue (HCF) life considerations or even mechanical failure. This phenomenon depends on the interaction between aerodynamics and structural dynamics; mainly due to the very high uncertainties regarding the details of the fluid flow through the component, it is very hard to predict accurately. In 2014, as part of the E-Break research project funded by the European Union (EU), an experimental campaign regarding the flutter behaviour of labyrinth seals was conducted at Centro de Tecnologias Aeronauticas (CTA). During this campaign, three realistic seals were tested at different rotational speeds, and the pressure ratio where the flutter onset appeared was determined. The test was reproduced using a linearized uncoupled structural-fluid methodology of analysis based on Computational Fluid Dynamics (CFD) simulations, with results only in moderate agreement with experimental data. A procedure to adjust the CFD simulations to the steady flow measurements was developed. Once this method was applied, the matching between flutter predictions and the measured data improved, but still some discrepancies could be found. Finally, a set of simulations to retain the influence of the external cavities was run, what further improved the agreement with testing data.