Many in the crowd booed as Pence entered the theater. Some also cheered and clapped as well.
At the end of the musical, the cast appeared on stage and cast member Brandon V. Dixon read a short statement directed at Pence. He thanked the vice president-elect for attending and asked the audience not to boo because "We're all here sharing a story of love."
"Vice President-elect Pence we welcome you and we truly thank you for joining us here at Hamilton, an American musical. We sir are the diverse America who are alarmed and anxious that your new administration will not protect us. ... But we truly hope that this show has inspired you to uphold our American values and to work on behalf of all of us."
He also noted that the show's cast is comprised of a diverse group of men and women of different colors, creeds and orientations.
Pence is a former governor of Indiana and former congressman who is known for conservative viewpoints on a range of issues, including opposition to expansion of LGBT rights.
Some critics on Twitter noted the contrast between Pence's views and the diverse cast, including the fact that the show's lead is an openly gay, HIV-positive actor.