The film, which stars Saoirse Ronan and is based on the novel by Colm Tóibín, tells the story of a young Irish girl who goes to the US to seek a new life.
It beat favourite to win, 45 Years starring Charlotte Rampling and Tom Courtenay. The award was presented by Friends star Mathew Perry to Brooklyn director John Crowley.
Idris Elba was named best actor on the night for Beasts of No Nation, while Maggie Smith was named best actress for The Lady in the Van.
The awards, held at the BBC’s former Television Centre in London drew big names from the acting world, including nominees Elba and Courtenay, Tuppence Middleton, Stanley Tucci, Matthew Perry, and Vanessa Redgrave.
Ronan is up for a Bafta and an Oscar for best actress for her role in Brooklyn.
Elba was presented with his best actor award by Redgrave. His film Beasts of No Nation is a harsh exploration of child soldiering in West Africa and Elba plays the charismatic but ruthless commandant of a boys’ army.
The Luther actor is also nominated for best supporting actor at the Baftas on 14 February.
He beat off stiff competition to clinch the award, including from double nominee Michael Fassbender for his performances as Apple founder Steve Jobs and Macbeth, Mad Max: Fury Road star Tom Hardy and Rampling’s co-star Tom Courtenay.
Brooklyn beat 45 Years, High-Rise, and The Lobster, which co-stars Colin Farrell.
The awards were hosted by TV presenter Simon Amstell.