On April 17, 2016, it was announced that Atkinson become the head coach of the Brooklyn Nets after the Hawks' season ended.

[12] Atkinson made his NBA head coaching debut on October 26, 2016, in a 122–117 loss to the Boston Celtics.

[13] He got his first win as an NBA head coach two days later when the Nets defeated the Indiana Pacers 103–94.

In Atkinson's fourth season with the Nets he led the team to a 28–34 record, before stepping down as head coach on March 7, 2020.

During the NBA Finals, the Charlotte Hornets offered Atkinson the position of head coach,[18] but he reportedly turned it down after informally agreeing to take the job.