He graduated from the music conservatory in Vienna. From 1909 to 1939, he served as music director at the Ljubljana Cathedral. Between 1908 and 1939, he was head of the organ school in Ljubljana.
He was a significant influence on the development of Slovenian church music. He was one of the most prolific Slovenian composers of the 20th century, publishing over 2,000 songs. On 24 September 1905 he composed the music for France Prešeren's patriotic poem Zdravljica. Premrl's composition soon prevailed as the most popular music for the song; by the 1940s, it had become one of the most popular Slovenian patriotic songs. In 1989, it was officially adopted as the anthem of the Socialist Republic of Slovenia, then officially part of former Yugoslavia. In 1991, it became the national anthem of independent Slovenia.
Stanko Premrl was the uncle of the Slovenian Partisan resistance fighter Janko Premrl, a.k.a. Vojko.