A compact dual ports antenna with high isolation is proposed for handheld radio frequency identification (RFID) reader which is rarely reported in open literatures. Different with conventional handheld RFID reader antennas with single port, the proposed antenna transmits and receives signal separately. The proposed antenna operating with full duplex mode can enhance effectively sensitivity of reader, since the strong transmitting signal of reader with single port is usually highly coupled with weak receiving backscatter signal of tag. The antenna utilizes E-shaped aperture-coupled patch structure that occupies less volume and provides further space-saving efficiency. The height of the proposed antenna is only 6.8 mm and the volume of that is 80 mm × 80 mm × 6.8 mm, which is easy to integrate in handheld RFID readers. The antenna uses two E-shaped coupling apertures to excite two orthogonal modes for dual-polarized operation. High isolation of around −30 dB is obtained by proper arrangement of the length of coupling apertures and the position of the stubs. The measured results show −10 dB matching band and −25 dB isolation band from 2.32 to 2.6 GHz and from 2.3 to 2.55 GHz, respectively. The antenna is suitable for applications in handheld RFID readers.