An accelerator-based neutron source powered by deuteron–Li (d–Li) reactions is among the most promising neutron sources for fusion materials irradiation facilities, such as IFMIF, IFMIF-DONES, and A-FNS. The yield estimation of neutrons and other particles is critical to the design of these facilities. Presently, the McDelicious code is employed for the aforementioned yield estimations, although it is not an open code. Recently, a deuteron-induced reaction library, JENDL/DEU-2020, was released by the Japan Atomic Energy Agency. Thus, employing benchmark tests, such as the Particle and Heavy Ion Transport code System (PHITS) + JENDL/DEU-2020, Monte Carlo N-Particle + JENDL/DEU-2020, and McDelicious, we confirm that PHITS (or Monte Carlo N-Particle (MCNP)) + JENDL/DEU-2020 effectively reproduces the experimental data and McDelicious results. We apply PHITS + JENDL/DEU-2020 to the yield estimations of the neutron, gamma, and charged particles in a Li target and to the yield estimation of the charged particles in the target backplate for A-FNS. The estimated production rates of tritium and 7Be during the continuous operation using a deuteron beam of 40 MeV and 125 mA are 1.4 × 1016 atoms/s (2.3 g/FPY) and 5.9 × 1014 atoms/s (0.21 g/FPY), respectively, and the estimated production rates of He and H in the target backplate for A-FNS are 3.2 × 102 and 1.8 × 103 appm/FPY, respectively.