The below answer contains spoilers (because the anime stops before this was explained).
To give you a little back story before explaining:
So after Ichigo is done with the Fullbringers, there is the Final Arc with the Quincies. Ichigo's Zanpaktou in Bankai is broken and he has to fix it with the help of the Zero Division. The man that creates the Zanpaktou tells him that he needs to find his true Zanpaktou, but Ichigo can't because he needs to learn something about his past that is blocking him.
This is how he learns about his father. In 10 chapters, his father finally talks so Ichigo could learn about his past, why he didn't tell him about his Shinigami powers and how his mother died.
Isshin was the former head of a branch of the Shiba Clan, as the Shiba that Rukia knew (Kaien Shiba), and Captain of the 10th Division. He was in the Shinigami world until Aizen, Gin Ichimaru and Kaname Tōsen were doing these experiments with Hollows and Shinigamis in the human world.
So after a while he decided to go to see what is going on in the human world (because people died), and he found a White (an experimental Hollow) and he couldn't defeat it. So Ichigo's mother came and she is revealed to be a Quincy and tried to defeat it. She did it, but she was injured by it, which infected her and she was becoming a Hollow.
So Kisuke found Ichigo's mother and father and told Isshin that if he wants her
to live he has to sacrifice his power to protect her in a device (as he did with the Vizards, but not 100% the same). He accepted and lost his powers and became a human. So when she died, he got his power back because it stopped protecting her.