The 32-year-old actress, who is engaged to entertainment lawyer Jamie Afifi, confirmed her pregnancy earlier this year.
Speaking to TV Guide, she said: "It's kind of a time cut into the future, so JD and I are already married and pregnant with our first kid.
"Bill [Lawrence] was very generous to write it in, so I'm not, like, carrying a giant chart or something in front of my belly all the time."
She added: "I'm going to do a bunch [of episodes] until this baby gets too big for me to go to work anymore."
Chalke will return to Scrubs for six episodes in January alongside co-star Zach Braff.