A method to assemble sandwich panels made of carbon fibre reinforced poly-ether-ether-ketone (CF/PEEK) facesheets and 3D-printed poly-ether-imide (PEI) honeycomb cores using induction welding is presented. Induction heating patterns inside CF/PEEK laminates of variable dimensions are first evaluated with a thermal camera and compared to a COMSOL Multiphysics model. Sandwich samples are then prepared by vacuum-assisted continuous induction welding under parameters selected from the modelling effort. Joining of sandwich panels made of CF/PEEK facesheets by induction welding under vacuum is demonstrated. Facesheets do not deconsolidate in the process and core crushing is avoided. Flatwise skin/core strength of the welded samples reaches up to 7 MPa, above reported performance for thermoset or thermoplastic composite sandwich panels.