Pulsating auroras (PsAs) appear over a wide area within the aurora oval in the midnight–morning–noon sector. In previous studies, observations by magnetometers on board satellites have reported the presence of field-aligned currents (FACs) near the edges and interiors of pulsating aurora patches. PsAs are thus a key research target for understanding the magnetosphere–ionosphere coupling process. However, the three-dimensional (3-D) structure of the electric currents has yet to be clarified, since each satellite observation is limited to a single dimension along its orbit. This study's aim was a reconstruction of the 3-D structure of ionospheric conductivity, which is necessary to elucidate the 3-D ionospheric current. Tomographic analysis was used to estimate the 3-D ionospheric conductivity for rapidly changing auroral phenomena such as PsAs. The reconstructed Hall conductivity reached its maximum value of 1.4 × 10−3 S m−1 at 94 km altitude, while the Pedersen conductivity reached its maximum value of 2.6 × 10−4 S m−1 at 116 km altitude. A secondary peak in the Pedersen conductivity, due to electron motion, at 9.9 × 10−5 S m−1 appears at 86 km altitude. The electron Pedersen conductivity maximum value in the D region was approximately 38 % of the ion Pedersen conductivity maximum value in the E region. The FAC, derived under the assumption of a uniform ionospheric electric field, was approximately 70 µA m−2 near the edge of the PsA patch. This FAC value was approximately 10 times that observed by satellites in previous studies. If the conductivity around the patch is underestimated or the assumption of a uniform field distribution is incorrect, the FAC could be overestimated. By contrast, due to sharper boundary structures, the FAC could actually have had such a large FAC.