The price was set this week at $24 a ticket for adults when the museum opens in May.
The memorial does not receive any federal funding at this time, and the admission price is the only way to keep the museum up and running.
The mayor says the museum deserves substantial government funding. "What could be a more nationally important site than this? It's a national tragedy and people come from all over the country, all over the world, to see it," said de Blasio.
The foundation board that oversees the lower Manhattan museum voted Thursday on the admission fee.
Families of Sept. 11 victims won't be charged. There will be discounts for children, seniors and schools.
It's still free to visit the memorial plaza with its twin reflecting pools. About 5.3 million people visited the plaza this year to see the two huge fountains that sit in the original footprints of the twin towers.
Some relatives of Sept. 11 victims have criticized the decision to charge for the underground museum, which houses relics of the terror attacks.
Foundation officials say charging admission is necessary to cover the $60 million a year it'll cost to operate the site.
The museum has raised $700 million for construction costs but hasn't gotten government funds for operations.
That $24 price is in line with other major tourist attractions in New York City. It costs $18 to take a ferry to the Statue of Liberty, $25 to see the Museum of Modern Art and $27 to visit the observation deck of the Empire State Building.
But the fee drew protests from critics, including some relatives of 9/11 victims, who said the high price would keep average Americans out. Unlike many other big museums in the city, there won't be the option of paying less than the "suggested donation."
Retired Deputy Fire Chief Jim Riches and Sally Regenhard, who each lost firefighter sons in the attacks, have lobbied for the entire site to be turned over to the National Parks Service.
"It was never intended to be a revenue-generating tourist attraction with a prohibitive budget and entrance fee," they said in a statement.
The Associated Press contributed to this report.