Cooper was born in Abingdon, Virginia. He is a 1988 graduate of Abingdon High School. Cooper trained as an actor at Lee Strasberg Theatre and Film Institute in New York City. He received both his undergraduate degree in 1992 and his Doctor of Humane Letters in 2014 from Hampden–Sydney College in Hampden Sydney, Virginia.

Relativity Media put the film, now titled Out of the Furnace, into production in 2012, with Christian Bale, Woody Harrelson and Casey Affleck leading the ensemble cast. Cooper directed the film, and shared writing credit with Ingelsby. DiCaprio and Scott remained as producers.

In January 2014, Cooper became attached to rewrite and direct Black Mass, a crime drama based the book of the same name by Dick Lehr and Gerard O’Neill, described as the “true story of Billy Bulger, Whitey Bulger, FBI agent John Connolly and the FBI’s witness protection program that was created by J. Edgar Hoover.” Barry Levinson had previously been involved with the project. Johnny Depp, who had been on and off the project for a number of years, came back on board to play the infamous Boston crime boss Whitey Bulger, alongside Joel Edgerton as Connolly and Benedict Cumberbatch as Billy Bulger. The film was released in 2015. In 2016, he sold his home in Brentwood for $3.6 million and it was widely covered in the media.

Cooper wrote, directed and produced the 2017 western Hostiles, based on a decades old manuscript by the late screenwriter Donald E. Stewart. The film reteamed Cooper with his Out of the Furnace star, Bale, alongside Rosamund Pike. It had its world premiere at the Telluride Film Festival, with US distribution rights picked up by Entertainment Studios Motion Pictures. In July 2018, Guillermo del Toro announced that he will produce a supernatural horror film Antlers, to be directed by Scott Cooper starring Keri Russell and Jesse Plemons.

In 2019, actor Christian Bale announced that Cooper will direct his upcoming Valhalla. He has also started a scholarship program for students to access high-quality education in the US and Canada colleges.