Abstract This work proposes a frequency‐selective surface‐based radome structure to selectively allow the radar altimeter operating band and also minimize the interference from Sub‐6GHz 5 G frequency bands. A Jerusalem cross and combinational loop (JCL) based frequency selective surfaces (FSS) unit cell of overall dimension 0.37λ was synthesized using a thin flexible substrate for use in fuselage of airborne systems. The proposed FSS unit cell exhibits transmission zero at 3.61 and 6.025 GHz and highly selective pass band at 4.3 GHz. The effect of bends and angle of incidence on the frequency response of the synthesized FSS was studied in transverse electric and transverse magnetic modes. A lumped element‐based equivalent circuit model for the proposed design was also presented. Finally, the fabricated prototype was experimentally validated in an Anechoic chamber setup and the suitability of the proposed FSS layers for aviation radar systems was confirmed.