Food irradiation is a clean, safe and non-thermal technology applied to destroy pathogenic microorganisms, i.e., Salmonella spp., in hen eggs. Currently, in Europe only the egg white can be irradiated up to 3 kGy, so different control methods are crucial for official inspections to identify illicit treatments. In this work, an analytical method was proposed to determine the radiolytic markers, namely 2–dodecylcyclobutanone (2–DCB) and 2–tetradecylcyclobutanone (2–TCB) in hen egg samples. This method is based on headspace solid phase micro-extraction coupled with gas chromatography/mass spectrometry (HS–SPME/GC–MS). The eggs were treated by an X-ray irradiator at dose levels of 0.5, 1.0 and 3.0 kGy. The preliminary validation showed good selectivity, without matrix interferences in non-irradiated samples. Spiked samples showed linear responses in the range 2.5–25.0 µg kg⁻¹, where 2.5 µg kg⁻¹ was the limit of detection for both analytes. Irradiated samples showed a dose-dependent increase in signal intensity and a constant 2–DCB/2–TCB ratio. The minimum dose level detected was 0.5 kGy for all samples, and the 2–DCB and 2–TCB signals remained stable over one month after irradiation. Not least, white analytical chemistry was used to evaluate the HS–SPME/GC–MS method validation effectiveness, greenness power and economic efficiency, compared to the EN 1785:2003 standard method. The results of this study prove that the HS–SPME/GC–MS method is a reliable green alternative to the official method, which is suitable in food safety control programs.