Czerny, who has led the dicastery since 2022, steps down because he reaches the mandatory retirement age of 80 on July 18 after helping lead the office since its 2017 launch.
Smerilli, 51, rises from secretary after earlier serving as undersecretary, while Baggio, 61, has been undersecretary since 2022 and was made a cardinal in December 2024.
The pro-prefect structure mirrors a 2025 precedent set when Pope Francis named the Vatican's first woman prefect, and Leo has continued that push with other senior female appointments this month.