Toomas Siitan graduated from the Estonian Academy of Music as a composer and received his PhD in musicology from the University of Lund. Since 1986 he has taught music history at the Estonian Academy of Music (since 2004 as a professor) and became in 2013 the head of the musicological department.
For many years, he was also the chair of the board of the Estonian Musicological Society and since 1999 has been vice chairman of the board of the Estonian Music Council. He is also active as a conductor as well as the artistic director of the Haapsalu Early Music Festival, a position held since 1994.
From 1976–1988, Toomas Siitan sang in the Estonian Philharmonic Chamber Choir (cond. Tõnu Kaljuste). Since 1990, he has been active as a conductor, leading collectives like the Estonian Philharmonic Chamber Choir, the Estonian National Male Choir, Haapsalu Festival Choir, the Estonian Radio Choir, the Chamber Choir of Estonian Choral Society, international choir Vox Europae and Tallinn Baroque Orchestra. In 1994 he founded the ensemble Studio Vocale.
His repertoire consists mainly of music from the 16th to 18th centuries, including large-scale vocal works such as the passions and cantatas by J.S. Bach and oratorios by Handel. In 2011 he was the musical director and conductor of the Johann Valentin Meder’s opera Die beständige Argenia.