The chamber confirmed Hahn 72-18.
Trump announced his intention to nominate Hahn as FDA commissioner on Nov. 1 after the departure of acting Commissioner Norman Sharpless. Brett Giroir has served as acting commissioner since Sharpless' departure.
Hahn is a oncologist who served as chief medical executive at MD Anderson Cancer Center in Houston.
Hahn told the Senate Health Education Labor and Pensions Committee he planned to address a rise in illnesses and deaths related to vaping.
"Dr. Hahn said to me he doesn't want to be known in history as the head of the FDA who saw this epidemic grow dramatically when it comes to vaping by young people," Sen. Dick Durbin, D-Ill., said, offering his support for Hahn.