Howard University, once among the top 100 on the U.S. News and World Report list of national universities, has fallen to 142nd in the magazine’s latest rankings published Tuesday.

The historically black university in Northwest Washington, which has weathered a recent period of turbulence, including a public split on the board of trustees over the school’s leadership and finances, was ranked 120th by U.S. News a year ago and 96th four years ago. Howard’s drop from 2012 to 2013 was the second-largest found in an analysis of the top 200 schools on the U.S. News national universities list.

“While I am concerned and we will look closely at the data, the U.S. News and World Report rankings represent one indicator of academic quality,” Howard President Sidney A. Ribeau, in office since 2008, said in a statement. He said several other indicators “speak to the exceptional quality of a Howard education,” including rising graduation rates and strong performances in the fields of medicine, dentistry, science and engineering.

The U.S. News rankings are probably the most closely tracked index of prestige in higher education, but they are also controversial. Critics say the rankings are based on flawed data and use a subjective formula that gives too much weight to a college’s selectivity and reputation.

U.S. News tweaked its formula this year, giving more emphasis to college graduation rates and less to the high school class standing of incoming students. The magazine’s methodology also factors in surveys of academic reputation and data on retention rates, college entrance test scores, financial resources and faculty resources, among other things.

On Aug. 22, President Obama said the federal government will aim, by autumn 2015, to rate colleges and universities on value, using such metrics as average tuition and loan debt, the share of low-income students they enroll, and graduates’ earnings.

On the U.S. News list, there were few major changes in the upper tier. Princeton ranked first and Harvard second, a year after they tied for first. Schools that made major moves up were Penn State University, jumping nine places to 37th, and Boston University, jumping 10 places to 41st.

Among schools in and near the Washington region, Johns Hopkins University (12th), Georgetown University (20th), the University of Virginia (23rd) and the College of William and Mary (32nd) each moved up one place.

“While these rankings never capture the true excellence of William & Mary, it’s always satisfying to see them move in a positive direction, as they did this time around,” said the college’s president, Taylor Reveley.

George Washington University, which had ranked 51st a year ago, was removed from that ranking in November after the revelation that it had overstated the high school credentials of its incoming freshmen. On Tuesday, it returned to the list at No. 52.

The University of Maryland at College Park, which ranked 58th last year, fell to 62nd. Virginia Tech (69th), American University (75th) and the University of Maryland Baltimore County (158th) — ranked the top “up-and-comer” school — all had better rankings this year. Catholic University dropped one place, to 121st, and George Mason University two places, to 141st.

“We went up a couple spots,” said Cornelius “Neil” Kerwin, president of American. “It’s hard to tell whether that’s a statistical artifact or something real.” But he said he was pleased to see the university show upward movement over several years.

Embargoed copies of the rankings were closely scrutinized Monday. “Listen, this is a cultural phenomenon,” Kerwin said. “Anybody who gets it will pay attention to it.”

It was not immediately clear why Howard fell 22 places this year, to 142nd. Rutgers, the State University of New Jersey at Newark, had the largest drop in the top 200, falling 27 places into a tie with Howard.

Howard ranked 115th in fall 2011 and 104th in fall 2010. From 2004 to 2009, it ranked in the top 100 every year but one.

In a letter made public in June, the vice chairwoman of the board of trustees, Renee Higginbotham-Brooks, said the university “is in genuine trouble,” citing financial challenges and management issues. Board Chairman Addison Barry Rand replied that Howard remains “academically, financially and operationally strong.”