Mats Malm is a professor of literary theory at the University of Gothenburg, AFP reported.
"I am very happy to be given this trust and look forward to the honorable commission as permanent secretary," he said.
Malm, 54, only joined the Academy four months ago.
He takes over from Anders Olsson, who has been serving as head of the Academy since June 2018 after the previous secretary, Sara Danius, was forced to step down amid a scandal sparked by Frenchman Jean-Claude Arnault, an influential figure on Stockholm's cultural scene.
Arnault, who is married to a then-member of the Academy who later resigned, was accused and later convicted of rape.
The 18-member Academy was split on how to handle its ties to Arnault.
Ugly public disputes ensued, several members quit, and the body was in such disarray that it ended up postponing the 2018 Nobel Literature Prize for the first time in 70 years.
The Academy has said it plans to announce the winner of the 2018 award together with this year's winner.