This paper proposes a procedure to design a flush air data system (FADS) for a stealth aircraft using wind tunnel testing based on the design of experiments (DoE) technique. The FADS of an aircraft reduces its radar cross-section (RCS) by preventing protrusion to its outer mold line (OML). The system acquires air data (e.g., altitude, airspeed, aerodynamic angles) by pressure measurements at multiple static holes. The wind tunnel testing is composed of two steps: the screening test for selecting influential factors and the database test for model construction. The 5-hole probe algorithm is used to predict the aerodynamic data out of pressure measurements. The FADS configuration design/optimization case study (pressure hole selection) is conducted.