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Harvard University expects to pay $49.8 million in federal taxes as a result of the tax reform package passed in 2017.

Most of the tax bill, $37.7 million, comes from the Tax Cuts and Jobs Act’s new tax on net investment income -- the so-called endowment tax. The other $12.1 million is from a net investment income tax on operational revenues, unrelated business taxable income and excise taxes on executive compensation.

The nearly $50 million tax bill is still an estimate, Harvard said in its annual financial report for the fiscal year ending in June 2019, which the university released Thursday. The federal government hasn’t issued final guidance that would allow the exact amount of tax to be calculated, but accounting principles require Harvard to book expenses in the year they were incurred.

Dozens of the country’s wealthiest colleges and universities are expected to be hit by the endowment tax, a 1.4 percent tax on earnings, although federal estimates anticipate 40 or fewer being affected immediately. Some institutions’ leaders have lobbied hard for a repeal of the tax, without any success to this point.

Harvard president Lawrence S. Bacow pointed to the investment tax as one of several factors that could hurt the university financially in a note at the beginning of the annual financial report.

“Uncertainty in federal research funding and the damaging tax on college and university endowments in the Tax Cuts and Jobs Act also have the potential to hinder Harvard’s ability to grow investments in financial aid, teaching, and research across campus,” Bacow wrote. “Our challenge is to acknowledge these realities, advocate for policies and laws that will support our mission and continue to manage our finances prudently and thoughtfully so that we can make the investments in students, faculty, teaching and research that make a positive and lasting impact in the world.”

Despite the new tax bill, Harvard’s net operating surplus rose almost 52 percent to $297.9 million in 2019. Total operating revenue rose nearly 6 percent to $5.5 billion as total student revenue rose 7 percent to $1.2 billion.

Factoring in nonoperating activities, the university’s net assets rose by $2.3 billion to $49.3 billion.

Harvard’s endowment totaled $40.9 billion at the year’s end, up from $39.2 billion. The endowment paid out at a rate of 5.1 percent, down from 5.2 percent in 2018 but within Harvard’s target range of between 5 percent and 5.5 percent.