SANTA CLARA — The San Francisco 49ers scored a major victory Wednesday when a county panel cut its Levi’s Stadium property taxes in half, but the fallout from its victory will hurt Santa Clara’s school district and several other public agencies that count on the revenue.

Specifically, the district and agencies will have to pay the team a total of $36 million in refunds by June and figure out how to make do with $6 million less a year in tax revenue from then on.

The Santa Clara County Assessment Appeals Board has issued a decision that drastically slashes the assessed value of Levi’s Stadium, a decision that County Assessor Larry Stone described Wednesday as “shocking and unexpected.”

Hardest hit is the Santa Clara Unified School District, which must give the 49ers a $13 million-plus refund in taxes to the team, followed by the county of Santa Clara, which owes $5.3 million, according to a memo released Wednesday by the county assessor’s office.

The preliminary ruling by the Assessment Appeals Board, issued in late November, is not yet final. But on Wednesday, Stone released a report estimating the impact to public agencies and held briefings for those that will be hammered by the decision.

“A 50% reduction for a single appeal is highly out of the ordinary. In my opinion, the AAB reached the wrong conclusion,” Stone wrote in a statement.

Santa Clara Unified School District officials learned the bad news from Stone on Wednesday morning, said district spokeswoman Jennifer Dericco. In addition to a $13 million one-time refund, the district will lose $2.5 million in tax revenue each year.

“Our one-time revenues this year and our funds from our reserve for just these types of budget uncertainties will carry us through this year, and adjustments to our budget assumptions in future year budgets will be made,” said Dericco in an email. “This is still disappointing news for the district to receive. Ultimately, the impact is on our students who would most certainly have benefited from that $13M and ongoing annual revenue.”

A major part of the dispute involves what’s known as possessory interest, or the extent to which the 49ers could privately benefit from using tax-exempt public property — Levi’s Stadium — and how much the team should pay in property taxes for that benefit.

Levi’s Stadium is owned by the city of Santa Clara and operated by the 49ers. A lease between the Santa Clara Stadium Authority and the 49ers splits primary scheduling rights between the two entities for six months at a time.

In its preliminary 10-page summary decision, the appeals board said it wouldn’t be accurate to determine possessory interest solely on the time the stadium authority and the team each uses Levi’s because the team’s profitability is influenced by the success of its business operations as well as real estate.

The appeals board concluded that the intent of both parties when they signed the lease “was to obtain rights of a balanced and equal value to each party,” and the 49ers have a 50 percent taxable interest in the stadium, not 100 percent as argued by the county assessor.

“The assessment appeals board agreed with Stadco (49ers) that they are effectively not getting any benefit from the property outside of the football season. I believe that is incorrect, and an oversimplification at the heart of a flawed conclusion,” Stone said in a statement.

In an interview late Wednesday afternoon, Stone said that even though the 49ers have primary scheduling rights for only half the year, he believes there is significant value to the team being able to control the facility and from the events it books outside the football season, such as concerts.

“Once you fully control a facility, then you have value — if it didn’t have value, then they wouldn’t care about it,” Stone said. He added that this is the largest property tax refund he can recall during his tenure.

It’s also one of the most complicated assessments his office has ever done, Stone said, and the appeal was the longest ever conducted in Santa Clara County, taking 21 days.

Rahul Chandhok, vice president of public affairs and strategic communications for the 49ers, said the team “accepts the decision.”

“Our focus, as always, will be on ensuring that Levi’s® Stadium continues to be a premier sports and entertainment venue for the region,” Chandhok said in an emailed statement.

It’s not clear when the appeals board will release a final decision with its complete findings of fact.

Normally, appeals board decisions on the market value of a property are final and there’s no additional legal recourse, said Deputy Assessor David Ginsborg. But in this case, the county could potentially file a lawsuit challenging the decision. First, however, the county needs to see the final ruling that lays out the board’s argument.

In addition to the school district and Santa Clara County, West Valley Community College will have to send a $3.14 million refund, the city of Santa Clara $2.86 million and the County Office of Education $1.38 million. Several other agencies will be paying back smaller amounts.

Staff writer George Avalos contributed to this report.

Contact Thy Vo at 408-200-1055 or tvo@bayareanewsgroup.com.