Fujifilm X-Pro3 has a 26.0MP APS-C (23.5 x 15.6 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor. On the other hand, Sony A6400 has a 24.0MP APS-C (23.5 x 15.6 mm ) sized CMOS sensor and features Bionz X processor.
Another difference between these two cameras is that Fujifilm X-Pro3's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the X-Pro3 and A6400 sensor size comparison.
Fujifilm X-Pro3 and Sony A6400 have sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Sony A6400 has 8% larger pixel area (15.28µm2 vs 14.12µm2) compared to Fujifilm X-Pro3, it has larger pixel area to collect light hence potential to have less noise in low light / High ISO images.