In this communication, a frequency reconfigurable directive antenna with low-radar cross section (RCS) property is presented. This antenna is composed of a slot-coupled microstrip patch and a two-layer metastructure. The top-layer metastructure integrates a partially reflection surface (PRS) with an absorbing surface, and the bottom-layer one consists of tunable reflection phase cells, which are loaded around the antenna source. The absorbing surface can absorb most of the incoming wave, and thus reduce the antenna RCS. The PRS and tunable reflection phase cells form a Fabry-Perot resonance cavity, making the antenna produce a highly directive beam. In addition, the operation frequency can be dynamically tuned by controlling the varactor diodes in the reflection phase cells. Both simulated and measured results have verified that employing the two-layer metastructure makes the antenna RCS largely reduced at a wide band ranging from 8 to 14 GHz. Compared with the traditional microstrip antenna, this antenna radiates a highly directive beam with gain enhancement of about 7 dB, and its operation frequency can be actively tuned from 9.05 to 10 GHz.