He started his career in the youth department of Zürich and played his first game as professional 7 April 1984 aged 18 in a 6–1 loss against Sion.

When Challandes was sacked, Fischer was appointed as caretaker 17 April 2010 and after three games, which he all lost, became permanent manager.

On 18 June 2015, Basel announced that Fischer had signed a two-year contract as first team manager.

[9] In the 2020–21 season, he led Union to a seventh-place finish, thus qualifying for the inaugural UEFA Europa Conference League edition.

In the 2021–22 season, he led Union to a fifth-place finish, thus qualifying for the UEFA Europa League for the first time ever in history.

[12] On 15 November 2023, after a bad start to the season including 14 winless competitive matches in a row, Fischer and Union Berlin decided to separate by “mutual agreement”.