BRUNSWICK — Bowdoin College has become the first college or university in Maine to have its endowment reach $1 billion, joining a select group of schools nationwide that have reached the billion-dollar threshold.

Having a healthy endowment is critical to allowing the school to provide the kind of educational programs it wants to offer while keeping student costs down, President Barry Mills said. Thirty-six percent of the school’s operating budget comes from the endowment, he said. Forty-five percent is restricted to student financial aid.

“The college really has to be affordable to the middle class to be sustainable for the long term,” Mills said.

College and university endowments represent donated money and other assets that are invested to grow over time and support college operations.

Endowments took a shellacking five years ago when financial markets tanked. Endowments at Maine universities and colleges lost close to half a billion dollars in value as the economy and stock market faltered.

But endowments have since rebounded, said Ken Redd, director of research and policy analysis at the National Association of College and University Business Officers. The most recent figures show that the average college endowment as of June 30, 2012, was $491 million, up from $372 million in 2009.

“The driving support behind a lot of the new money in endowments has been fundraising, as well as investment returns,” he said.

Maine’s three largest college endowments have shown strong growth the past few years.

Bowdoin’s endowment has risen from $688 million in 2009 to more than $1 billion, while Colby College’s stood at an estimated $650 million this June, up from $453 million three years earlier. Bates College’s endowment is estimated to have been $233 million in June, up from $184 million in 2009.

As of June 30, 2012, 71 U.S. colleges and universities had endowments of $1 billion or more, according to the latest figures from NACUBO. The 2013 figures become available in January.