Tenth-grader Bobby McKeithen died from his injuries sustained in the shooting at Butler High School in Matthews, about 12 miles southeast of Charlotte.
Police said the shooter, 16-year-old Jatwan Cuffie, who was a classmate, was taken into custody.
Cuffie admitted he shot McKeithen to a teacher, according to authorities.
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"I am heartbroken to hear that we have lost a student to school violence in one of our schools," said State Superintendent Mark Johnson. "We have contacted Charlotte-Mecklenburg authorities and will assist in any way we can, but of course our first thoughts are for the parents and other loved ones of the student who passed away. The safety of our students is paramount. This is a sad day for all of North Carolina, and we must work together as a community to address these problems."
"I am heartbroken to hear about today's school violence that has taken the life of a high school student in Matthews, and my family is praying for this community," Governor Roy Cooper said in a statement. "I have been in touch with local officials to offer condolences and state support as needed. As we get more information it is critical that we come together to do everything in our power to prevent these incidents from happening and keep guns out of our schools."
Police believe the shooting was an "isolated incident" and have recovered the weapon.
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Dozens of parents gathered outside of the school of about 2,000 students to wait.
Lockdown was lifted around 9:15 a.m. and students streamed out, many crying and hugging parents.