Mayor Bill de Blasio’s hefty subsidy to run the city’s beleaguered ferry service is the second highest in the nation, according to a report released Monday.

Among ferry systems with over one million annual trips, NYC Ferry lagged behind only New Orleans in terms of public subsidies, according to the Citizens Budget Commission.

De Blasio’s budget calls for a $9.34 per-ride ferry subsidy.

NYC Ferry also came in second nationwide in terms of operating expenses covered by fares — just 24 percent.

For comparison, the city’s Staten Island Ferry — which the city Department of Transportation provides to riders free of charge — receives $5.46 per rider in government subsidy.

Ferry operators in San Francisco, meanwhile, spend just over $4 per rider and recover 60-plus percent of operating costs from the fare box.

Higher fares are the key to sustainable finances, CBC analyst Sean Campion told The Post.

“The big difference is fares. The fares that [other cities] offer vary by route, so that routes that are longer and have higher operating costs, or serve a smaller number of people, tend to have higher fares,” Campion said.

“The city should at least consider options to make the system more sustainable,” he added.

The CBC’s analysis comes on the heals of ridership data released last week, which found ferry-goers to be overwhelmingly white and rich.

In a statement, the de Blasio administration defended its investment — and noted that the subsidy dropped 13 percent in the last year.

The city has spent $673 million to build and operate the ferries, which launched in 2017. Officials said they expect the per-ride subsidy will eventually drop to between $7 and $8.

“The NYC Ferry is overwhelmingly popular with riders, a testament to the need it fills,” said de Blasio rep Seth Stein.

“Like any brand-new transportation system it required an up-front investment and popular routes in order to expand to more under-served areas.”