Johanna Sinisalo was born in 1961 in Helsinki, Finland. She studied piano and composition at the Sibelius Academy, and she received her Ph.D. from the University of Helsinki in 1991. Her doctoral thesis dealt with the relationship between music and language and was published as a book in 1996 by Finnish Academy Publishers
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Her other scholarly publications include a study on 18th-century music history and a work on the life of composer Jean Sibelius. Since 1996, Sinisalo has been a professor of musicology at the University of Helsinki. In 2005 she became the director of the Sibelius Museum, which was founded by her uncle Jean Sibelius in 1917 to preserve the composer's legacy and works for future generations.
Sinisalo is a member of Finland's Academy of Sciences and Letters, an honorary member of the Finnish Composers' Association, and an honorary member of the Finnish Music Society.