Non-destructive eddy current evaluation is a practical and well-established tool in aerospace and other industries, used to find or identify material defects not otherwise detectable. It can also be employed to measure the thickness of various coatings, although it is not yet fully optimized for multi-layer thermal spray systems, such as thermal barrier coatings (TBCs). The first part of this paper aims to look at the underlying mechanisms of the eddy current thickness measurement technique and uses a Design of Experiment (DoE) study to identify key characteristics related to thickness measurement of thermal barrier coatings. The second part of the paper is a case study on the application of the findings into general production, showing the achieved improvements in accuracy and repeatability of thickness measurements.