The Academy awards the Helmholtz Medal and the Leibniz Medal. With these awards, it honours, respectively, outstanding lifetime scholarly achievements, and special services in the support and promotion of scientific work.

In this it continues a longstanding tradition of the Prussian Academy of Sciences. The Helmholtz Medal was awarded for the first time on the 2nd of June 1892 to the physiologist Emil Du Bois-Reymond, the physicists Robert Bunsen and Lord Kelvin and the mathematician Karl Weierstraß. The first Leibniz Medal was awarded to the Berlin art collector James Simon, a sponsor of excavations and patron of museums.