Gerstner was born in Komotau in Bohemia then part of the Habsburg Empire (present-day Chomutov in the Czech Republic).

After that he studied mathematics and astronomy at the Faculty of Philosophy at the Charles-Ferdinand University in Prague between 1772 and 1777.

In 1795 Gerstner became a member of the government commission which tried to improve higher technical education in the Austrian empire.

The construction of this railway was started in summer 1825 by his son Franz Anton (Ritter) von Gerstner (1796, Prague - 1840, Philadelphia).

The polytechnic school founded by Gerstner exists till today as the Czech Technical University in Prague (ČVUT).

The institute for artificial intelligence and cybernetics research at ČVUT bears the name Gerstner Laboratory.