Ten students and a teacher were injured, six of them critically. It was the third fatal shooting incident in a US school in five months, bringing the death toll to nine.
"I do think we've reached a point where we have to analyse these incidents to see whether or not we can learn anything," said President Clinton.
Flowers and candles were left outside the Westside Middle School in Jonesboro, Arkansas, after Tuesday's shootings. Classes were cancelled indefinitely.
Authorities said Mitchell Johnson, 13, and his cousin, Andrew Golden, 11, donned camouflage gear and armed themselves with rifles before Golden triggered the school's fire alarm. As classmates and teachers filed outside 27 shots were fired at them.
One student Brandy George said: "We thought it was just firecrackers," then he said, "I saw one of my teachers get shot." Classmate, Jamie Clevenger, said Johnson had said he "had a lot of killing to do".
Three 12-year-olds and an 11-year-old, all girls, were killed and pregnant teacher Shannon Wright, 32, who was shot as she tried to shield a student from a bullet.
"There's no explanation, in my opinion, why an 11-year-old or 13-year-old would do something like this," said Craighead County Sheriff Dale Haas.
Prosecutors were deciding if the boys would be tried as adults. Under Arkansas law, children under 14 who are convicted of a crime must be released once they turn 18.