Eight other girls were wounded, and CNN has reported one of them had since died.
Police anticipate the death toll to rise even further, saying some of the others are so badly wounded they may not survive.
Monday's attack, at the Amish school in the small town of Nickel Mines, is the third deadly US school shooting in the past week.
US President George W Bush said he was "deeply saddened" by the tragedy, and has ordered an emergency conference on school violence next week.
Roberts is not believed to be Amish, himself.
‘Revenge’ attack
The gunman has been identified by authorities as milk truck driver Charles Carl Roberts.
Roberts had ordered 15 boys and some adults in the one-room schoolhouse to leave, then lined up tied up 11 young girls with wire and plastic cables.
It’s reported he then lined his victims against the blackboard and opened fire, systematically executing three of them before killing himself.
It is believed the four who died were all shot in the head, as were some of the injured.
Roberts, a father-of-three, told his wife that he was exacting revenge for something that happened 20 years ago.
He left a rambling suicide note and letter to his family, referring to an event 20 years ago for which he sought revenge, and he planned for a lengthy siege.
Commissioner Jeffrey Miller of Pennsylvania state police said that in a final conversation with his wife before killing himself, Roberts also spoke of his need for "revenge".
"He was angry with life and was angry at God ... there may have been a loss of a child at some point in his life," Commissioner Miller said.
He did not elaborate, but local media have reported Roberts had a fourth child who died as an infant.
Weaponry
Police said Roberts had carefully planned his assault, and was armed with an arsenal of guns and other weapons.
During his shooting rampage, he fired three rounds from a shotgun and 13 from a 9mm semi-automatic pistol.
He also had a rifle, 600 rounds of ammunition, a stun gun, two knives and tools including a hammer, a hacksaw, pliers, wire, eye-bolts, rolls of tape and a bucket with a change of clothes.
While a hostage negotiator was trying to call the man's mobile phone, Roberts opened fire and about 10 police troopers stormed the class room.
They found the gunman dead along with the bodies of three girls.
Amish reaction
One of the dead was believed to be a girl working as a teacher's aide. The Georgetown School classroom had 26 students aged six to 13.
Commissioner Miller said that of the injured: "It would be a miracle if we were somehow able to have no further loss of life."
The tragedy has stunned Nickel Mines, a largely Amish community about 100 kilometres west of Philadelphia.
There descendants of settlers of Swiss-German stock have preserved a religious lifestyle that shuns aspects of modern life like cars and electricity.
Amish farmers live simply, travel by horse and buggy and cultivate the land using old-fashioned traditions.
The Amish community was today struggling to come to terms with its devastating loss.
"We will mourn in our own way, quietly," said Amish fencer John Fisher, 33.
"We will pull together. We will do what needs to be done. Whether it's crops to tend to, or animals to feed, or comforting the victims. There's times you don't need to make words."
Daniel Beiler, 30, said the incident was having a "severe impact" on the community of about 300 people.
"I just don't know how to react to it yet," he said. "I'm just in a daze. We've never had a problem like this before. It makes us a lot more close-knit community."