Sep. 24–Once again, the rich get richer.

Harvard’s $19.3 billion endowment, the largest in the country, yesterday reported that its investments grew by 12.5 percent in the year ended June 30, a performance that ranks among the best in the nation.

“Their numbers are off the top of the charts,” said Richard Charlton, the president of New England Pension Consultants, a Cambridge firm that provides advice to large institutional investors. Charlton said Harvard’s 12.5 percent gain would almost certainly put it among the top 1 percent of all big institutional funds, a group that includes endowments, pension funds, and foundations.

Harvard’s gain came in a year when the stock market was essentially flat and the typical big investment fund recorded a rise of 4 percent. Although many universities have not publicly released their numbers, the Chronicle of Higher Education recently reported that on average university endowments rose less than 3 percent last year.

The Massachusetts Institute of Technology last week said it would cut its budget and lay off 200 people because of losses suffered by its endowment over the past three years.

For Harvard, being on top of the heap is nothing new. During both the bull market of the 1990s and the bear market of the past three years, the Harvard endowment has done significantly better than the competition. Harvard Management Co., which runs the endowment, said its performance over the past five years and 10 years would rank it among the top 5 percent of comparable funds. Looking at the same numbers, Charlton said Harvard probably ranks in the top 1 percent for both periods.

“Jack Meyer has an incredible long-term record,” said Scott Henderson, a Boston attorney who once ran the pension fund for the state of Massachusetts. Meyer has been the president of Harvard Management for the past 13 years.

Harvard runs its endowment differently from most of its peers. Meyer and a staff of 180 people manage about 55 percent of the money themselves.

Most big funds farm out all their investments to professional money managers. To keep its talent, Harvard Management pays Wall Street-sized salaries. In a good year a few of its top money managers can earn more than $10 million.

Only 15 percent of the endowment’s assets are invested in the American stock market. The rest is divided among a wide range of asset classes, including real estate, hedge funds, commodities, venture capital and foreign stocks and bonds.

The endowment doesn’t try to time the market. Neither does it make big bets on interest rates or credit quality. Despite that, Harvard’s bond managers last year earned a return of 30 percent in domestic bonds and more than 50 percent in foreign bonds.

In a note explaining the performance numbers, Meyer attributed the big gains to Harvard’s “ability to capture perceived mispricings among a broad array of fixed-income instruments.” Meyer said his bond managers can do particularly well in unsettled markets.

Last year Harvard had negative returns in only two areas: foreign stocks, which declined 3.8 percent and private equities, down 5.2 percent. Private equities are investments in businesses that are not public companies.

Over time, the superior returns have made a huge difference to the university. In his note Meyer said that if his money managers had recorded average investment returns over the past 10 years, Harvard’s endowment would be $9.6 billion smaller than it is today.

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