The roots of the orchestra go back to 1701, to the founding of the Academia Philharmonicorum, which performed oratorios and other works of the era.
On 23 October 1908, the Filharmonična družba officially merged with the Glasbena matica (The Music Society) to form the first incarnation of the Slovenian Philharmonic Orchestra, which lasted from 1908 to 1913.
The new version of the orchestra gave its first concert on January 13, 1948, conducted by Salvador Bacarisse and attended by composer Marjan Kozina, who became the first administrator of the Slovenian Philharmonic Orchestra.
The orchestra employed a number of "permanent conductors" (stalni dirigenti) from its 1948 re-inception, including Jakov Cipci (1948–1955), Samo Hubad (1948–1966), Bogo Leskovic (1951–1958), and Lovro von Matačić (1955–1956).
The first non-Slovenian principal conductor of the orchestra was George Pehlivanian, from 2005 to 2008.