Stock was born in Jülich, Germany and given his early musical education by his army bandmaster father. At the age of fourteen, Frederick Stock was admitted into the Cologne Conservatory as a student of violin and composition, where he counted Engelbert Humperdinck as one of his teachers, and Willem Mengelberg among his classmates. After graduating from the conservatory in 1890, Stock was accepted to the Municipal Orchestra of Cologne as a violinist.

In 1895, Stock met with Theodore Thomas, director of the then fledgling Chicago Symphony Orchestra and the man who was to have a decisive impact on Stock's future. Thomas, who was then visiting Germany in search of recruits for his Chicago Symphony, auditioned Stock and gave him a position as violist in the orchestra. Thomas soon realized, however, that his new violist was also a very talented conductor and in 1899, Stock was promoted to assistant conductor.

After the sudden death of Theodore Thomas in 1905, Frederick Stock took over the post of music director of the Chicago Symphony. That year, he wrote a symphonic poem Life, "in memory of Theodore Thomas". At first filling in the position only on a temporary basis, Frederick Stock finally assumed the role of permanent music director in 1911 only after the Chicago Symphony's board of directors failed to persuade Gustav Mahler, Hans Richter, Felix Weingartner, Karl Muck, and Felix Mottl, among others, to take over the position.

Under Stock's direction, the Chicago Symphony became one of America's top orchestras, developing a distinctive brass sound that can already be heard in the orchestra's first recordings.

An enthusiast of modern music, Stock championed the works of many then modern composers including Mahler; Richard Strauss; Stravinsky, whose Symphony in C was commissioned for the orchestra's 50th anniversary; Sergei Prokofiev, who was soloist in the world premiere of his Third Piano Concerto in Chicago; Gustav Holst; Zoltán Kodály, whose Concerto for Orchestra was commissioned by Stock; Nikolai Myaskovsky; Josef Suk; William Walton; Arthur Benjamin; George Enescu; and many others.

Frederick Stock's thirty-seven year tenure as head of the Chicago Symphony was surpassed in America only by Eugene Ormandy's lengthy directorship of the Philadelphia Orchestra. Soon after Stock's death in Chicago on 20 October 1942, Désiré Defauw was chosen as his successor.

In 1916 the Chicago Symphony, under Stock's baton, made its first set of recordings for the Columbia label. In fact, these recordings were the first ever made by an American orchestra under its music director. The orchestra would later record for RCA Victor, then go back to Columbia, only to finally go back to RCA Victor in 1941-1942 for its final series of recordings under Stock.

The orchestra's first electrical recordings were made in 1925, including a performance of Karl Goldmark's In Springtime overture; these early recordings were made in Victor's Chicago studios and within a couple of years the orchestra was recorded in Orchestra Hall. Stock's last studio recording, Ernest Chausson's Symphony in B minor, was released posthumously in 1943.