The Bavarian State Orchestra emerged from one of the oldest orchestras in Germany. Its origins can be traced back to the year 1523, when the composer Ludwig Senfl took over the direction of the Munich Kantorei. The first renowned director of Munich's Court music, and of the Court Orchestra, was the composer Orlando di Lasso, who was officially hired in 1563, during the reign of Duke Albrecht V. In 1594, the Duke established a seminar for musical studies, with scholarship for the gifted sons of farmers and average citizens without means, to insure the future of the Court Orchestra. After Lasso's death in 1594, Johannes de Fossa, the former Assistant Musical Director, took over leadership of the orchestra.

After over 100 years in which the orchestra's repertoire was comprised mainly of church music, the first opera performance took place in Munich: Maccioni's L'Arpa festante, performed in the Residence in 1653. The composer Agostino Steffani earned his reputation with many performances of italian operas in the 1680's.

The term "orchestra" was not introduced until 1762. The court orchestra, directed by Andrea Bernasconi, first began to do regular opera work in the middle of the 1770's, as numerous performances began to take place on specified days. In 1778, Mannheim's Elector Karl Theodor introduced his government's legacy to Munich. He brought 33 of Mannheim's court musicians with him to Munich; on October 1st, 1778, these Mannheim musicians were united with 32 selected members of the Munich Court Orchestra.

In 1811 the Musical Academy, made up of members of the Court Orchestra, was founded.

The same year saw King Max I laying the cornerstone of the Royal Court and National Theatre, which was opened on October 12th, 1818 During King Max I's reign, the duties of the Court Orchestra included in equal measure the performance of church music, teatime music, chamber music and theatre music. Under King Ludwig I, the orchestra managed to win Franz Lachner as its first Generl Music Director in 1836.

The reign of King Ludwig II is cloesly allied with the name of Richard Wagner. On June 10th, 1865, the Court Orchestra Director Hans von Bülow conducted the premiere of Tristan and Isolde; on june 21st, 1868, that of Die Meistersinger von Nürnberg. There followed premieres of das Rheingold and Die Walküre, conducted by Franz Wüllner, on September 22nd, 1869, and June 26th, 1870 respectively.

Hermann Levi was the General Music Director from 1872 to 1896. Since then, the most important artists of their time have served as heads of the orchestra, from Richard Strauss, Felix Mottl, through Bruno Walter, Hans Knappertsbusch, and Clemes Keauss, to Georg Solti, Ferenc Fricsay, Joseph Keilberth, and Wolfgang Sawallisch. Zubin Mehta has been head conductor and Bavarian General Music Director since 1998.

Starting with the 2006/2007 season, Kent Nagano has become Zubin Mehta's successor as Bavarian General Music Director.