In this work, an efficient slotted waveguide antenna (SWA) system is designed for S-band high power microwave (HPM) applications. The designed SWA comprises of 10-slot elements placed on the broad wall of SWA with a modified Gaussian distribution (MGD), integrated with two inside-grooves and a Gaussian dielectric radome of high-density polyethylene (HDPE) material. The inside-grooves are introduced to suppress the surface current on the waveguide, which results in high gain as well as sidelobe level (SLL) reduction in the E-plane. The MGD controls the SLLs, and the unique Gaussian profile shape radome offers constant radiation characteristics. The proposed antenna system, within existing size constraints, offers a high gain of 20.1 dBi in conjunction with a high-power handling capability of greater than 100 MW. The designed SWA system has compact dimensions of 8.46λ0× 1.38λ0× 1.50λ0, with SLLs of −20 dB and −22 dB in the H- and E-plane, respectively. The HPM antenna system, radiating at 3 GHz, is fabricated on aluminium material using the milling process. The simulated SWA system has good agreement with measured results. Moreover, the proposed SWA system offers clear advantages in terms of its robustness, design simplicity, high power handling capability, and high gain.