The 46-year-old American actress, who has been the darling of this award season, was a favourite to win the Oscar for her powerful performance in the movie that took 12 years to make.
Arquette, who is vocal on prejudices plaguing the showbiz industry, stressed on the right of women to equal wages in Hollywood in her acceptance speech.
"Ok. Jesus. Thank you to the Academy, to the powerful and beautiful nominees, our whole cast and crew, my Boyhood family... I dedicate this to all the women who gave birth," said Arquette as Meryl Streep stood up to applaud her speech.
Her award was presented by last year's best supporting actor Oscar winner Jared Leto.
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The acclaimed drama saw Arquette playing Olivia Evans, a doting and ambitious mother of Mason Evans, Jr (Ellar Coltrane) and his elder sister Samantha (Lorelei Linklater) despite her many failed marriages.
The actress has previously won Los Angeles Film Critics Association Award, New York Film Critics, National Society of Film Critics Award, Golden Globes and BAFTA for her performance before taking home the coveted golden statuette.