Abstract Boron neutron capture therapy (BNCT) is a radiation therapy that selectively kills cancer cells at the cellular level using the boron neutron capture reaction (BNCR) (10B(n.α)7Li). The amount of boron 10 B delivers in boronophenylalanine (BPA)‐BNCT to achieve anti‐tumor effects is ≈15–40 ppm. The same is true for all boron drugs; however, whether the same amount of 10 B is required for other boron drugs with different accumulation characteristics has not been intensively investigated. Therefore, herein, a virtual cell model with intracellular organelles is prepared, and the BPA equivalent dose concentration to the cell nucleus is analyzed using particle and heavy ion transport code system‐based microdosimetry. Additionally, the intranuclear minimal region (IMR) is set as a reference for the concept of the intranuclear domain in the microdosimetric kinetic model, and the BPA equivalent dose concentration to the IMR is estimated. The required boron delivery dose greatly varies depending on the dose assessment based on the accumulation characteristics of boron agents in intracellular organelles. Evaluation of the BNCR effect according to the accumulation characteristics without being influenced by the specified value of 15–40 ppm is recommended.