The actor also took a shot at Donald Trump "for making black people number one on the most oppressed list."
The actor has received tons of praise for his hit series Atlanta, which was also nominated for Outstanding Comedy Series. Glover portrays Earnest "Earn" Marks on the FX show, which sees his character navigating the hip hop world of Atlanta.
It was the second win of the evening for the actor, who made history earlier during the ceremony, becoming the first Black person to win an Emmy for Outstanding Directing for a Comedy Series.
While accepting his award, Glover casually announced that he was expecting baby number two. "I want to thank my baby, my son, for just being the joy of my life. I want to thank my unborn son, we're listening to Stevie tonight."
The actor and Altanta creator also took a shot a Donald Trump, jokingly thanking the president "for making black people number one on the most oppressed list, he's the reason I'm probably up here."
Glover is the first Black actor to win the award for comedy lead since 1985, when Robert Guillaume took home the award for Benson.