This work presents a new miniaturized frequency selective surface (FSS) design to be employed as an electromagnetic (EM) shield in the 2.45 GHz (ISM band) range, with optically transparent glass substrate. A step‐by‐step procedure on the miniaturization technique and the corresponding frequency response is presented. The proposed FSS layout consists of an optimized square loop and a central reactive element consisting of meandered lines. The metal layout is embedded between borosilicate glass as substrate on top and bottom sides, achieving a final periodicity of 0.12λ. A miniaturization of 69.05% was achieved, and the equivalent circuit model was synthesized to understand the EM behavior of the proposed FSS design, and results were compared. The shielding effectiveness of 53.25 dB was achieved with polarization insensitivity for both TE and TM modes, and the angular stability was also studied. A prototype of the proposed work was fabricated, and the frequency characteristics were studied in the anechoic chamber setup. Ellipsometer setup was used to study the optical properties of prototype, and optical transparency of 81.8% was achieved. The measured and simulated results show close agreement and confirm the usability of the proposed FSS in glass‐based electromagnetic interference (EMI) shielding applications in ISM band.