A compact magnetron cavity having integrated optics is designed and realized for a rubidium atomic clock that is being developed for the Indian Regional Navigation Satellite System. This cavity comprises a cylindrical dielectric cell with 25 mm diameter and 25 mm height. The cavity is designed to resonate at the rubidium hyperfine ground-state frequency of 6.8346 GHz with TE011-mode. A loop gap resonator structure is employed to obtain the required uniform mode along the quantization-axis in the cavity. The cutoff frequency of the cavity is designed in such a way that the influence of optics on the cavity mode is negligible and it is well within the tuning range of the cavity. The measured results of the realized cavity match up to 90% with the RF simulation results. The overall volume and mass of the realized cavity are about 86 cm3 and 120 g, respectively, making it suitable for portable space based applications.