As the noise got louder and closer, school officials warned over the intercom system that it wasn't a drill.
Authorities are now clearing the school "room by room", the Daily Times reported.
The sheriff's department said in a Facebook post that morning that Aztec High School was being locked down and evacuated. No other injuries were reported, and it was not clear if the shooter died by suicide or was killed by police.
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The New Mexico State Police were taking over the investigation. Nearby schools in the area have also been put on a preventative lockdown, AP reported.
Aztec police chief Mike Heal told reporters that the suspect was down, without clarifying if "down" meant injured, dead or in police custody.
Aztec High School is about 180 miles northwest of Albuquerque, New Mexico.
"We all know each other in San Juan County", she added.