The drone market’s growth poses a serious threat to the negligent, illicit, or non-cooperative use of drones, especially in airports and their surroundings. Effective protection of an airport against drone intrusions should guarantee mandatory safety levels but should also rely on a resilience-driven operational concept aimed at managing the intrusions without necessarily implying the closure of the airport. The concept faces both safety-related and security-related threats and is based on the definitions of: (i) new roles and responsibilities; (ii) a set of operational phases, accomplished by means of specific technological building blocks; (iii) a new operational procedure blending smoothly with existing aerodrome procedures in place. The paper investigates the evaluation of such a resilience-driven operational concept tailored to drone-intrusion features, airport features, and current operations. The proposed concept was evaluated by applying it to a concrete case study related to Milan Malpensa Airport. The evaluation was carried out by real-time simulations and event tree analysis, exploiting the implementation of specific simulation tools and the assessment of resilience-oriented metrics. The achieved results show the effectiveness of the proposed operational concept and elicit further requirements for future counter-drone systems in airports.