The 17-year-old student, whose name was withheld because he is a juvenile, was arrested and jailed Tuesday on charges of inciting destruction of life or property, Jefferson County Sheriff John Stone said.
The arrest comes as Columbine High School marks the six month anniversary of the tragic shootings.
Former student Brooks Brown says he knows the student and says he and all students at Columbine are under enormous stress.
"He has been grouped in with killers. He has been hated by the school because people are afraid he's going to do it again, and you can only take so much of that," Brown said.
Investigators seized a diagram of the school and other writings from the senior, who last year helped Columbine gunmen Eric Harris and Dylan Klebold produce videos foreshadowing their assault.
Officials with the Jefferson County school district said they contacted the sheriff's department after hearing rumors about the boy's threats.
Rick Kaufman, executive director of communications for the Jefferson County School District, said there had been a number of rumors circulating both in and out of school that led to the student's arrest.
"We take all threats very seriously," whether the threats are made in jest or not, he said.
A student reported that the teen had remarked that he would "finish the job started by Eric Harris and Dylan Klebold," Stone said.
Kaufman said that due to the anniversary and the new threat, security has been stepped up at the school.
Twelve students and a teacher were killed when Harris, 18, and Klebold, 17, hurled bombs and scattered gunfire at the school on April 20. After the rampage, the gunmen committed suicide.
The student has been suspended, faces expulsion, and is being held on $500,000 bond. The teen-ager also faces a misdemeanor charge of theft for allegedly stealing a school microphone.
"The district will continue to enforce its zero tolerance policy against threats of violence," the school district said in a press release.
There is no indication that any other students were involved in the threats, school officials said.
Some parents were notified of the threats Tuesday night and about 450 students did not show up for school, school officials said. That is about a quarter of the high school's 2,000 students. The normal absentee rate is about 5 percent.
Prosecutors asked for the unusually high bail because, "we just felt this particular one was a safety-to-the community thing," said Mark Pautler, Jefferson County's chief deputy district attorney.