Thermoset composites are widely used for the manufacturing of modern composite aircrafts. The use of thermoplastic composites (TPC) in aerospace applications is, however, gradually increasing owing to their cost-effectiveness in manufacturing and improved damage tolerance. An example of the use of thermoplastic composites in aircraft is the thousands of clips and cleats that connect structural elements in the fuselage of new composite passenger aircrafts, which are press formed from preconsolidated laminates in only a few minutes. Thermoplastic composite and thermoset composite parts are currently joined through mechanical fastening, which is known not to be an optimal joining technique for composites. Nevertheless, the ability of TPC to be welded with little surface preparation and short assembly times poses the question of whether thermoplastic and thermoset composites can be welded together. Hybrid thermoplastic to thermoset composite welding poses two main challenges: firstly, adhesion between the thermoplastic and thermoset resins; secondly, degradation of the thermoset resin when exposed to the welding temperatures. This paper presents a procedure to successfully prevent any negative thermal effects on the thermoset resin during high-temperature welding of thermoplastic to thermoset composites. The procedure is based on reducing the heating time to fractions of a second during the welding process. In order to achieve such short heating times, which are much too short for commercial welding techniques such as resistance or induction welding, ultrasonic welding is used. A particularly challenging scenario is analysed by considering welding of carbon-fibre reinforced poly-ether-ether-ketone (CF/PEEK), with a melting temperature of 340°C, to carbon-fibre reinforced epoxy (CF/epoxy) with a glass transition temperature of 157°C.