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, Canon 90D has a 33.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features DIGIC 8 processor.
Canon 90D's sensor provides 7MP more than Fujifilm X-Pro3's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
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 90D sensor size comparison.
As seen above, Fujifilm X-Pro3 has a 1.1x Larger sensor area than Canon 90D. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.