The 9/11 Memorial and Museum’s first full year of operation ended in the red, with costs outstripping revenues by $25.2 million, The Post has learned.

The private nonprofit foundation, chaired by former Mayor Mike Bloomberg, racked up $108 million in expenses but took in only $87.3 million, just-filed 2015 tax records show.

The negative bottom line stems largely from a drop in revenues as government grants used to construct the museum were spent.

The foundation received only $17 million in grants and contributions in 2015 but raked in $61.8 million from the sale of tickets, tours, memberships and souvenirs.

The memorial, where twin pools mark the fallen Twin Towers, is open to the public at no charge, but the museum charges $24 admission, or $15 to $18 for seniors, veterans, students and youths. Close to 6 million people have visited the museum.

The museum’s gift shop, which sparked controversy for selling 9/11-themed T-shirts, jewelry and dishware — including a since-discontinued cheese plate — took in $5 million, the records show.

The foundation easily covered the budget gap. Total assets dropped from $729.7 million in 2014 to $705.2 million.

Spokesman Michael Frazier dismissed the shortfall.

“We are not operating at a deficit,” he said, adding that 94 percent of the cash expenses were covered by “earned revenue” and the rest by contributions.

Among the $108 million in expenses, the foundation counted $38.3 million for “depreciation, depletion and amortization” of its equipment and furnishings.

That left $69.6 million in cash outlay.

For years, foundation officials said it would cost $60 million to run the memorial and museum.

“That was an early projection before our first full year of operations,” Frazier said.

Sandra Miniutti, of the watchdog Charity Navigator, confirmed the tax filing shows “the organization spent more than it brought in” that fiscal year, even though the claimed $38.3 million in depreciation is not a day-to-day expense.

Salaries and benefits jumped from $18.3 million in 2014 to $22.2 million, largely because staffing increased after the museum opened in May 2014, Frazier said.

Some employees also got raises. The biggest paycheck went to CEO Joe Daniels, who took home $543,050 in compensation in 2015, up from $489,266 in 2014.

Daniels, who has held the position since 2006, announced in June that he plans to step down, but he remains on the job. A successor has not yet been selected, Frazier said.

The foundation also paid an Atlanta firm $9.5 million to provide security. That does not include the cost of NYPD and Port Authority officers who patrol the site.

In February, the House passed a bill to grant up to $25 million a year to the foundation. A Senate subcommittee on national parks has yet to vote on the measure, which critics call a disguised earmark. The full Senate must approve the bill by Dec. 31 or it dies.