The President is the head of the Academy. He or she must be an ordinary member. The President is elected by a plenum of the ordinary members of the Academy for a term of three years. The President may be re-elected. 

The nuclear medicine specialist Markus Schwaiger has held the position of Academy President since 2023. His long line of predecessors began in 1759 with Sigmund von Haimhausen, and continued with well-known figures including Max von Pettenkofer, Friedrich Wilhelm Joseph Schelling and Walther Meißner. The office of President was an honorary one for many years, but in 2017 it became a full-time position.