Zachariah Blanton was arrested earlier in the day and was jailed in Jackson County.
He faced preliminary charges of murder, attempted murder and criminal recklessness, prosecutor Stephen Pierson said.
Blanton, of Gaston, admitted to the sniper shootings during questioning by investigators, but a motive was unclear, State Police Superintendent Paul Whitesell said. It was not immediately known whether Blanton had an attorney.
Blanton came to the attention of investigators late Monday after an acquaintance told a Delaware County deputy that the teen might be involved in the shootings, Whitesell said. Detectives then searched Blanton's home and found a rifle of the same caliber used in the shootings.
"The weapon we obtained was precisely what we were looking for," Whitesell said.
A message seeking comment was left for Blanton's grandparents, who police said where his legal guardians.
Blanton's great-aunt told The Star Press of Muncie that she was shocked by the allegations against him. "I can't imagine that he would be involved," Denise Blanton said.
The two sniper victims were hit early Sunday as they rode in pickup trucks on Interstate 65 near Seymour, south of Indianapolis.
About two hours later, bullets struck a moving tractor-trailer and a parked sport-utility vehicle on I-69 in Delaware County, about 100 miles to the northeast near Blanton's home. No one was hurt in those shootings.
The FBI joined the investigation Monday as investigators searched fields, overpasses and roads looking for evidence. Detectives from Columbus, Ohio, who helped solve that city's 2003 and 2004 sniper shootings also traveled to Indiana to help.
Phillip Gardner, principal of the 300-student Wes-Del High School in rural Delaware County, said word of Blanton's arrest was "just tragic."
He described Blanton as an average student who played football and was a shot putter for the track and field team. He said the teen was on course to graduate next spring.
"I know he was into mechanics," Gardner said. "He had a big, old four-wheel truck that he was driving all the time. That kind of kid."
The principal said he could not talk about whether Blanton had faced any disciplinary action at the school.