In this paper, we propose a polarization-selective electromagnetic (EM) transparent mesh-type E-shaped antenna unit-cell in a shared aperture. The proposed antenna unit-cell, which can be expanded to a larger array in a modular way, has one S-band antenna on the upper layer and nine X-band antennas on the lower layers. The simple E-shaped structure, which has a low profile with a good bandwidth, is used for the antenna elements. However, due to the limited aperture size of the stacked configuration, the lower-layer elements can be physically blocked by the upper-layer element. To reduce this blockage effect, the S-band element is rotated 90 degrees with respect to X-band elements so that the polarizations between the S- and X-band elements are perpendicular to each other. Moreover, to minimize performance degradation due to the blockage effect, a mesh structure is applied for S-band elements for EM transparent characteristics, thereby improving EM transparency from −30 dB to −1.5 dB. The extended via cavity wall is also employed outside the nine X-band elements to minimize the mutual coupling and to reduce antenna size. To confirm the effectiveness of the proposed design, the proposed antenna unit-cell is fabricated, and the radiation characteristics are measured, in a full anechoic chamber. The average bore-sight gains in the S- and X-band are 5 dBi and 4.5 dBi, respectively. The results confirm that the proposed design is suitable for shared-aperture radar applications.