Born in Olbernhau, Saxony, Kretzschmar was son of the organist and cantor Karl Dankegott Kretzschmar and Karoline Wilhelmine, née Leupold. He was from 1862 a student in the Kreuzschule in Dresden, where from 1867–1868 he was twice Prefect of the Dresdner Kreuzchor. In addition, from 1870 he studied Philology at Leipzig University as well as Music at the Leipzig Conservatory and was awarded his doctorate there. From 1871 he was actively teaching in Theory, Composition, Piano and Organ at the Leipzig Conservatory, and acted as director/conductor for various musical societies. In 1876 he spent a year as theatre orchestra conductor in Metz, and undertook research expeditions in England and Italy for the study of musical history; from 1877 to 1887 he was Director of Music at the University of Rostock, and city music director there from 1880.
From 1887 to 1904 he renewed his position in Leipzig as active University Music Director. From 1888-1898 he was Director of the RiedelChoral Society. In the year 1890 he was awarded an honorary professorship, and in 1890 he founded the Leipzig Academic Concerts which he conducted until 1895. In 1904 he was appointed as regular Professor of Music at the University of Berlin, and from 1907–1922 he was Director of the Royal Institute for Church Music. From 1909 to 1920 he was Director of the Königlich Akademischen Hochschule für ausübende Tonkunst founded in 1869, later the Musikhochschule Berlin. In 1912 he was elected Chairman of the :de:Musikgeschichtliche Kommission|de:Preußische Musikgeschichtlichen Kommission and thus the editor of the Denkmäler deutscher Tonkunst. This historical music edition was begun in 1892 by Brahms, Joachim and Philipp Spitta. He was a government privy counsellor. One of his students was composer and musicologist Walter Niemann.
Hermeneutics
Kretschmar founded the discipline of musical hermeneutics in around 1900. According to the musicologst Maria Fuchs,
Death
He died in Berlin-Schlachtensee in 1924, after which he was buried in a grave of honour in the :de:Evangelischer Kirchhof Nikolassee|de:Protestant Nicholassee churchyard of the :de:Kirche Nikolassee in Berlin.
In his novel Doktor Faustus, Thomas Mann creates the character of Dr Wendell Kretschmar, the inspirational and eccentric musicologist, lecturer and teacher of the composer Adrian Leverkühn. The name is probably given in homage to his real-life contemporary Hermann Kretzschmar, whose essays in musical interpretation were widely read and appreciated around the turn of the twentieth century.