The 16-year-old allegedly snuck into the room at Central High School in St. Joseph and carried out the disgusting deed on March 15.
He was caught by a hidden security camera and now faces charges of third-degree assault.
Cops claim his sick joke came to light after staff complained their coffee had a weird "chemical taste."
Headteacher Melody Smith searched through surveillance footage, spotted the possible culprit and called police.
"We are distraught that this has forced a couple of our teachers to go through an unbearable situation. It is a repulsive situation," Smith told KCTV5.com.
The two teachers who drank the urine are now undergoing tests in case the liquid was infected with a disease.
The teen, who has also felt the wrath of fellow student who said his prank "wasn't funny," will appear in juvenile court on April 30.