SummaryMultiple input multiple output (MIMO) constitutes a wireless approach that employs several senders and receivers in order to send numerous data at once. Due to the rapid increase of cellular mobile device usage and the limitation of computing power, antenna selection (AS) has attracted more and more attention recently. AS can keep a balance between communication performance and computational complexity. In this paper, a novel deep learning (DL)‐based AS for MIMO software defined radio (SDR) system is proposed. The main objective of this work is to select the optimal antennas in MIMO systems to balance the efficiency of communication and maximize the secrecy capacity in massive MIMOME channels. First, we set up a DL‐based AS‐aided MIMO SDR environment that ensures intelligent decisions for AS. Accordingly, the hybrid loss function induced in bidirectional long short term memory (HLFI‐Bi‐LSTM) model is proposed to build the decision server, in which it takes some estimated features as input. The features such as channel state information, received signal strength indicator (RSSI), signal‐to‐noise ratio (SNR), and antenna gain are considered accordingly as the input to HLFI‐Bi‐LSTM. The HLFI‐Bi‐LSTM model is the extended version of Bi‐LSTM, which is improved by inducing the hybrid loss function, which is the combination of two functions namely, combo loss and inverse mean square error. The proposed HLFI‐Bi‐LSTM attained the greater accuracy value of 0.968 at 80% for optimal selection of the antenna.