Johann Fischer was the son of Jonas Fischer, the piper of Augsburg. He received a musical education from his father and the protestant cantor Tobias Kriegsdorfer (1608-1686). From 1661 to 1664 he was the student of Samuel Capricornus, the choir master of the Wurttemberger court in Stuttgart. After his death, Fisher worked as a copyist for Lully in Paris and so became familiar with his style. He returned to the court choir in Stuttgart in 1673. The following year he moved to Augsburg to serve as a church musician. During his time in Augsburg he produced 60 works of church music.
In 1683 Fischer accepted a three-year position at the court of the Duke of Ansbach as a violinist, teacher and composer. He held a similar position in Mitau (present-day Jelgava in Lithuania) from 1690 to 1697 at the behest of Duke Friedrich Kasimir of Kurland. After the choir dissolved he lived for a time in Riga. In the late 1690s he travelled across Europe. In 1700 he took up a position in Luneburg, in 1701 he performed for the king of Poland, in 1702 he was the Duke of Mecklenburg-Schwerin’s concert master. In 1704 he was disappointed by a trip to Copenhagen, where he’d hoped for a position in the royal court. In 1707 Fischer appeared in Bayreuth and later lived in Stralsund, Stockholm and Stettin. In the last years of his life he was choir master for Margrave Philipp Wilhelm of Brandenburg-Schwedt. According to Johann Mattheson, Johann Fischer lived to be seventy.