The head of the Zoological Institute is its Director. The Director manages the institute, organizes its institute within their competence, and is responsible for its activities. The current Director of the Zoological Institute is Prof. Nikita Chernetsov.

In order to preserve the continuity and ensure the development of academic tradition, the position of the Research Director has been introduced at the Zoological Institute. The Research Director of the institute is Prof. Oleg N. Pugachev, director of the Zoological Institute in 2006-2018.

The director of the Zoological Institute has two deputies for research. The deputy directors are Prof. Sergey Yu. Sinev and Dr. Igor G. Danilov. The director of the Biological Station Rybachy Dr. Andrey L. Mukhin is also a deputy director of the Zoological Institute. Furthermore, the director has a deputy for Zoological Museum. This position is filled by Ms. Milena N. Tretiakova. Mr. Yuri A. Grigorev is the deputy director for general issues; he provides managerial and technical support of the Zoological Institute.

The institute provides for the position of an Academic Secretary; the director of the institute determines their duties. The Academic Secretary of the Zoological Institute is Dr. Natalia N. Bezborodkina.