Words that count days use an exceptional reading. Even though this is a jukugo word, it uses kun'yomi readings for both the kanji. Think about this word this way:
The circus is in town this weekend and you can't wait to get there. You want to show off your new foots car (ふつか) to all the circus clowns. But you have to use your feet to get it there and it ends up taking you two days! Darn this old fashioned foots car!
I will go see a movie with my older sister on the second day of next month.
It's been two days since the prince followed the puppy and disappeared in the woods of Mt. Fuji.
If you study diligently, two days is enough to learn hiragana.