The brothers were part of a group touring the campus when campus police detained them for a pat-down. They were eventually released, but missed the rest of the tour. School officials say the parent of another prospective student called the police on them because they apparently made her "nervous."
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Critics are holding up the incident as just the latest example of racial profiling.
"This incident is sad and frustrating from nearly every angle, particularly the experience of two students who were here to see if this was a good fit for them as an institution," CSU officials said.
They arrived a little late because the teens took the family's only car and drove seven hours from New Mexico to Fort Collins, Colorado, to visit the campus on Monday, their mother told reporters. She said they'd saved their own money to make the trip.
"This was their dream school and I wanted to give them that opportunity," said the mother Lorraine Gray.
By the time they showed up, the tour had already begun.
"A parent participating in the tour called campus police because she was nervous about the presence of two young men who joined the tour while it was in progress," the school said. "When the police confirmed the brothers were part of the tour, they let them rejoin the group. But by that time, the tour had moved on."
"It breaks my heart, because they didn't do anything to warrant that," Gray told reporters. "They're walking on their own ancestors' land, so it breaks my heart."
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Colorado State officials said they are working to ensure there's not a repeat of such an incident. They are inviting the two teenagers back to the school, saying it will pick up the tab for them to travel back there for a VIP tour with their family.
The school also said Friday it would refund the money the brothers spent to travel to the school for Monday's tour.
"As a university community, we deeply regret the experience of these students while they were guests on our campus," they said. "The fact that these two students felt unwelcome on our campus while here as visitors runs counter to our principles of community."
Colorado's Lt. Gov. Donna Lynne said her office was concerned as well. Lynne also serves as the chair of Colorado's Commission on Indian Affairs.
"We want to reiterate our commitment to ensuring our public universities are open and welcoming to all students and hope that the young men will not be deterred in their pursuit of attending college in Colorado, a traditional homeland to many tribal nations," Lynne said.
The Associated Press contributed to this report.