"Our employees are worried this law will impact them," Moynihan said on CNBC'S "Closing Bell" Thursday afternoon. "We think it ought to be repealed."
However, he stopped short of saying whether Bank of America would pull jobs from North Carolina if the legislation went unrepealed.
The statehouse beef has drawn international attention since North Carolina enacted House Bill 2 — better known as the "bathroom bill" — a law that prohibits people from using restrooms that do not correspond with the sex on their birth certificates.
Since being signed into law by North Carolina Governor Pat McCrory in March, the legislation has been criticized for unfairly targeting transgendered individuals.
Bank of America isn't alone on Wall Street in its opposition of the legislation.
Other banks, including Deutsche Bank, Citigroup and Wells Fargo all issued statements calling for the repeal of the bill in the days and weeks following its passage. Silicon Valley piled on, with companies including Paypal, scotching plans to expand within North Carolina and citing the bill for their decision.
The legislation has also cost North Carolina revenue from various concerts. Musicians including Pearl Jam and Bruce Springsteen have cancelled shows in protest of HB2.
Earlier this week, the rhetoric surrounding the bill was ramped up, with Attorney General Loretta Lynch and the U.S. Department of Justice suing the state, saying HB2 is a violation of the U.S. Civil Rights Act of 1964. McCrory and another state officials filed a suit against the DOJ the same day, saying their suit was "a baseless and blatant overreach" that stemmed from a "radical interpretation" of the Civil Rights Act.
"This action is about a great deal more than just bathrooms," Lynch said earlier this week in prepared remarks. "It was not so very long ago that states, including North Carolina, had signs above restrooms, water fountains and on public accommodations keeping people out based upon a distinction without a difference."
Moynihan demurred when asked who he supported for president, but said he would like to see "reasonable tax reform" and "reasonable immigration policy" in the next administration.
"We need a president and a country focused on growth," he said on CNBC.
Moynihan also said there will "absolutely" be more cost-cutting ahead for the bank.
"It is hard work to keep reengineering the company and keep taking out the costs and doing it carefully so we serve customers," he said.
Bank of America is down about 80,000 people in the last five years, he said.