Carroll, an Aurora Democrat who served as majority leader, was a unanimous choice and will become the second woman in state history to lead the Senate.
Sen. Rollie Heath, a Boulder Democrat, will be majority leader.
Carroll will need final confirmation as president from the entire Senate once it reconvenes in January. Democrats now hold a single-seat majority in the chamber.
The vote comes as the Democratic caucus reels from the recalls of former Senate President John Morse of Colorado Springs and Sen. Angela Giron of Pueblo.
Both Morgan Carroll and Rollie Heath were ousted from office in September in the wake of their support of stricter gun laws that Democrats passed in the last legislative session.
Another Democratic state senator, Evie Hudak of Westminster, is currently the subject of a renewed recall effort.