The new system also tweaks the way a charity’s administrative expenses, or overhead, are evaluated. Under the current system, charities can’t score a “perfect” 10 points on that measure unless they had zero administrative expenses, which isn’t realistic in most cases. Under the new system, charities can get a 10 if they score within a given range for their type of nonprofit group. Ms. Searing said the change helps charities avoid “starving themselves” to avoid the appearance of high overhead.

The change in the overhead rating also means that it’s now possible for groups to score a perfect 100 points over all — and 49 charities will do so, Mr. Thatcher said.

Nearly three-quarters of charities will not see a change in their overall ratings under the revised system. About 19 percent of charities will see their ratings go up, while about 8 percent will go down. “There’s always going to be someone who’s unhappy,” Mr. Thatcher said.

Mr. Thatcher said the advisory panels help strike a balance, allowing input from professionals who know the nonprofit sector while guarding against any undue influence that might skew ratings. “You don’t want to get too close to any individual charity,” he said.

Here are some questions and answers about assessing charities:

Should I worry if my favorite charity’s rating drops?

“We don’t advocate that a donor jump ship if a rating changes,” said Sandra Miniutti, vice president of marketing for Charity Navigator. Rather, she said, a change suggests that donors should seek more information from the charity and see if it offers a good explanation. In that way, she said, donors can educate themselves about the charity and decide over time if they want to continue supporting it.

Why doesn’t Charity Navigator rate a charity’s operational effectiveness?

Charity Navigator’s long-term goal is to add a “results reporting” component, or an assessment of how effective each charity is in accomplishing its mission. That takes time, since each type of charity may use different criteria. “The hard part,” Mr. Thatcher said, “is figuring out just what each should be measuring.”

What other sources are available to help me assess a charity?

Other sources for information on nonprofit organizations include BBB Wise Giving Alliance, CharityWatch, GuideStar and GiveWell.