The federal civil rights lawsuit was filed Sunday against the Pearland Independent School District and the three staff members of Berry Miller Junior High who used the marker to color the student's scalp.
The three claimed that his "common African American 'fade' haircut violated the Pearland ISD dress code policy," the lawsuit reads.
The school's assistant principal threatened to suspend the boy if he did not have his scalp design colored. The design stood out even more when that was done, so school personnel proceeded to color his entire scalp with black marker.
"They laughed as they took many minutes to color 13-year-old J.T.'s scalp which took many days of scrubbing to come off. J.T. was immensely humiliated and shamed," the lawsuit states.
"There are hardly any African Americans in America with jet black skin and, of course, neither does J.T.," the court document reads.
"It is commonly understood among scholars and the general public that depicting African Americans with jet black skin is a negative racial stereotype. During the Jim Crow era [of racial segregation] slaves were often depicted as happy in their slave existence and with jet black skin as a means to disguise their humanity and imply that they are unlike 'white' people."
As news of the incident spread and outrage grew, the Pearland ISD issued a statement saying that it was "extremely disappointed to learn of a situation," but insisted that the boy's hair cut violated district dress code.
Nevertheless, a "campus administrator mishandled disciplinary action," and the practice that is "not condoned by the district," it said. The unnamed administrator was placed on administrative leave over the incident.
The statement said that ISD officials contacted the student's family "to express our sincerest apology and extreme disappointment in this situation."
However, according to the lawsuit and the school website, the assistant principal involved in the incident has since been promoted to school principal.
In a related incident southeast of Pearland, in Galveston, Texas, two white police officers on horseback were recently photographed in early August leading a handcuffed African-American by a rope -- a scene that evoked past lynchings of black people.
Those officers will not face a criminal investigation for their actions, officials said.
