Gubaidulina was born in Chistopol, in the Tatar ASSR. In her youth she would spend much time praying in the fields near her home that she might one day become a composer. She studied composition and piano at the Kazan Conservatory, graduating in 1954. In Moscow she undertook further studies at the Conservatory with Nikolay Peyko until 1959, and then with Shebalin until 1963. She was awarded with Stalin-fellowship. Her music was deemed "irresponsible" during her studies in Soviet Russia, due to its exploration of alternativetunings. She was supported, however, by Dmitri Shostakovich, who in evaluating her final examination encouraged her to continue down her "mistaken path". However, she was allowed to express her modernism in various scores she composed for documentary films, including the 1968 production, On Submarine Scooters, a 70mm film shot in the unique Kinopanorama widescreen format.
In the mid-1970s Gubaidulina founded Astreja, a folk-instrument improvisation group with fellow composers Viktor Suslin and Vyacheslav Artyomov. In 1979, she was blacklisted as one of the "Khrennikov's Seven" at the Sixth Congress of the Union of Soviet Composers for unapproved participation in some festivals of Soviet music in the West.
Gubaidulina became better known abroad during the early 1980s through Gidon Kremer's championing of her violin concerto Offertorium. She later composed an homage to T. S. Eliot, using the text from the poet's spiritual masterpiece Four Quartets. In 2000, Gubaidulina, along with Tan Dun, Osvaldo Golijov, and Wolfgang Rihm, was commissioned by the Internationale Bachakademie Stuttgart project to write a piece for the Passion 2000 project in commemoration of Johann Sebastian Bach. Her contribution was the Johannes-Passion. In 2002 she followed this by the Johannes-Ostern ("Easter according to John"), commissioned by Hannover Rundfunk. The two works together form a "diptych" on the death and resurrection of Christ, her largest work to date. Invited by Walter Fink, she was the 13th composer featured in the annual Komponistenporträt of the Rheingau Musik Festival in 2003, the first female composer of the series. Her workThe Light at the End preceded Beethoven's Symphony No. 9 in the 2005 proms. In 2007 her second violin concerto In Tempus Praesens was performed at the Lucerne Festival by Anne-Sophie Mutter. Its creation has been depicted in Jan Schmidt-Garre's film Sophia - Biography of a Violin Concerto.
Since 1992, Gubaidulina has lived in Hamburg, Germany. She is a member of the musical academies in Frankfurt, Hamburg and the Royal Swedish Academy of Music.