Kaepernick will appear in the series and add his own voice to the project.
The limited series will run for six episodes and reunites DuVernay with Michael Starrbury, who will write and act as executive producer.
DuVernay and Starrbury previously worked together on "When They See Us," which received 16 Emmy nominations.
In 2016, Kaepernick made national news when he refused to stand up while the National Anthem played before the NFL games. He said he did it to protest the police shooting of African American men and other social injustices facing blacks in the United States.
He added: "Colin's story has a lot to say about identity, sports and the enduring spirit of protest and resistance. He couldn't be happier than telling this story to the Netflix team."
Netflix has yet to announce an official release date for the series.