This works offers a polarization-insensitive, wide angular stable, and wideband electromagnetic interference shielding structure using an integration of frequency selective surface (FSS) with magnetic substrates. The equivalent circuit model (ECM) together with the analytical model is derived to figure out the physics of the shielding structure. The overall inductance of the shielding structure is increased using a magnetic ferrite sheet and magnetic silicon rubber sheet as substrates. Further, four different deep neural network configurations are investigated with inverse modeling to predict the shielding structure parameters within a fraction of seconds. The mse between expected and predicted output is only 2.92 × <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$10^{-8}$</tex-math></inline-formula> . The entire X-band is shielded with a minimum 10-dB shielding effectiveness (SE) and with SE of 56 dB at resonance. The FSS unit cell size is only 0.21 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\lambda$</tex-math></inline-formula> × 0.21 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\lambda$</tex-math></inline-formula> . Furthermore, the proposed shielding structure shows stable transmission performance up to <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$75^{\circ}$</tex-math></inline-formula> angle of incidence for both perpendicular and parallel polarization. Finally, a prototype is fabricated and measured using nondestructive free space measurement. Good agreement among the simulated, ECM, analytical model, and measured results demonstrate the efficacy of the proposed technique for building an effective shielding structure.