Gerstner predominantly played in the Second Bundesliga. In the 1989–90 season, he played for FC 08 Homburg in the Bundesliga. During this season, he scored his only first division goal on 22 August against FC St. Pauli. The next three years, he played for second division side VfB Oldenburg, who were almost promoted in the 1991–92 season.
Towards the end of his playing career, he was a player-manager for FC Carl Zeiss Jena in the 1998–99 season. After the end of his playing career, he managed SV Straelen from 1 October 2002 to 30 June 2003.
From August 2006 to June 2006, he was with oberliga club FC Schönberg 95. After the end of his contract in Schönberg, he became the new assistant manager of Austrian club SK Sturm Graz. On 24 June 2009, he became the manager of the newly relegated Second Bundesliga team Arminia Bielefeld. His contract ran until 30 June 2010, but on 11 March 2010 Arminia Bielefeld officials dismissed Gerstner. The team was then managed by caretakers Frank Eulberg and Jörg Böhme until the end of the season. On 28 February 2011, Gerstner took over Kickers Offenbach, but he was fired after two months due to lack of success.