Mary Dempsey has headed the library system for 18 years. She says she is retiring to spend more time with her family.
The new boss is Brian Bannon, who was the chief technology officer of the San Francisco library system.
This comes just after the mayor tried to restrict library hours then backed off part way to leave them open on Mondays.
The mayor now says the library system has to look to the future.
"We have to figure out how our libraries and branch libraries, which are so important to our neighborhoods, can adapt, change and prosper in the new information age," said Chicago Mayor Rahm Emanuel.
"I think the libraries have a great opportunity to explore and understand how people are changing the way they learn and incorporate that in the core services we provide in the physical space as well as online," said Bannon.
Publisher Linda Johnson Rice was also named head of the library board of directors.