What cartoon show had a girl rabbit and stupid funny boy rabbit. It was on later at night. Around 2000 or 2001?

You're likely thinking of "The Wild Thornberrys" which aired on Nickelodeon from 1998 to 2004.

* Eliza Thornberry, the main character, is a girl who can talk to animals.

* Donnie Thornberry, her younger brother, is known for being clumsy, naive, and often getting into trouble.

While it wasn't strictly a "later at night" show, it did sometimes air in later time slots.

Do the details of Eliza and Donnie fit what you remember?