In this paper, a deep-learning based power/EM analysis attack on the state-of-the-art RSA–CRT software implementation is proposed. Our method is applied to a side-channel-aware implementation with the Gnu Multi-Precision (MP) Library, which is a typical open-source software library. Gnu MP employs a fixed-window exponentiation, which is the fastest in a constant time, and loads the entire precomputation table once to avoid side-channel leaks from multiplicands. To conduct an accurate estimation of secret exponents, our method focuses on the process of loading the entire precomputation table, which we call a dummy load scheme. It is particularly noteworthy that the dummy load scheme is implemented as a countermeasure against a simple power/EM analysis (SPA/SEMA). This type of vulnerability from a dummy load scheme also exists in other cryptographic libraries. We also propose a partial key exposure attack suitable for the distribution of errors inthe secret exponents recovered from the windowed exponentiation. We experimentally show that the proposed method consisting of the above power/EM analysis attack, as well as a partial key exposure attack, can be used to fully recover the secret key of the RSA–CRT from the side-channel information of a single decryption or a signature process.