The study did not look at the reasons for the decline, but its lead author, Brian Kit of the Centers for Disease Control and Prevention, said the theory made sense.
The research, released online Tuesday by the Journal of the American Medical Association, also showed that children's average overall cholesterol levels declined slightly.
Too much cholesterol in the blood raises the risk of heart disease. It isn't usually an immediate threat for most children, but those who have the problem often grow into adults with a high risk.
Kit and his colleagues drew data from an intensive national study that interviews people and does blood-cholesterol tests. They focused on more than 16,000 children over three periods - 1988-94, 1999-2002, and 2007-10.
In the most recent period studied, 1 in 12 children ages 6 through 19 had high cholesterol, down from 1 in 9 during each of the earlier periods - roughly a 28 percent decline.
The average overall cholesterol level fell from 165 to 160. In children, 200 is called too high.
The study was the first in almost 20 years to show such a decline. Children's cholesterol levels also fell between the 1960s and the early 1990's, probably because people were eating less fat.
The researchers in the latest study detected modest improvements in children's levels of so-called good cholesterol, which can protect the heart. That may be partly due to declines in teen smoking and childhood exposure to secondhand smoke over the last decade. Studies have found that chemicals in cigarette smoke can lower good cholesterol.
The bigger news was what happened with bad cholesterol and triglycerides. They went down by small but significant amounts.
Cholesterol levels have been declining in adults, too.
But cholesterol-lowering drugs known as statins were a big part of the reason for that decline - millions of adults take them. Children are rarely given statins.
Artificial trans fats are known to decrease good cholesterol and increase bad cholesterol. In 2006, the federal government began requiring that packaged foods list the amount of trans fat per serving, a boon for careful shoppers.
Meanwhile, a push to take trans fats out of foods gained momentum. Cities such as Philadelphia and New York City have banned artificial trans fats at restaurants and other places serving food, and California in 2010 became the first state to adopt such a ban. Even Crisco, the goopy shortening that was trans fat incarnate, was reformulated to take it out.
Despite the good news, experts remain worried.
Seventeen percent of U.S. children are obese, perhaps because they are still eating lots of carbohydrates and sugar. That, along with little exercise, can lead to diabetes and heart disease.