Kevin Lein was wounded in the arm and was in good condition, Holbeck said.
The student, whose identity was not disclosed by police and has not yet been charged, was tackled by two school employees and is in custody, Holbeck said.
The incident happened when the student came into a main office and got into some kind of disagreement with the principal, according to Sioux Falls Police Officer Sam Clemens. There was a physical struggle and the teenager took out a firearm and shot Lein, added Clemens.
The assistant principal and the school's athletic director quickly tackled the teenager, Holbeck said, and kept him under control until authorities arrived.
And they came in droves -- including agents from the FBI and ATF, several sheriffs and police agencies and officers with the U.S. Department of Homeland Security, according to Clemens.
The school, meanwhile, went into its often drilled procedure, Holbeck said, with panic buttons pushed and students put in lockdown.
Bomb squad investigators were still checking out the school midday Wednesday as a precaution, Clemens said, but believe that the building is safe. Police have recovered the firearm, he added.
Holbeck has not made a decision on whether school will be in session Thursday.
Lein, meanwhile, is recovering. He even called Holbeck from the hospital.
During that conversation, the wounded principal even asked the superintendent how he was doing, Holbeck said.
"It's a shame that for years schools have been trying to prepare for this and you hope it doesn't happen in your backyard," the superintendent said.