School Department investigators have determined that several racially charged incidents involving Boston Latin School students were mishandled by administrators, including one accusation against a student with whom the headmaster has a personal connection, according to an official with knowledge of the review.

The accused student allegedly ridiculed two female students, one white and one African-American, the Globe has learned.

Headmaster Lynne Mooney Teta, in an interview Friday, said she was informed of an allegation involving the accused student about a year and a half ago. She said she was told there was one girl involved, not two.

And, she said, the incident had nothing to do with her decision this week to resign.

Teta said the student was 13 and in the eighth grade at the time of the alleged incident, which she said occurred outside of school time. She said the incident was immediately addressed by the assistant headmaster responsible for the eighth grade, and an objective supervisor from the district’s central office also reviewed the case to ensure that protocols were followed. The student was disciplined at the time, and there has been no further incident, she said.

School officials are prohibited, under a confidentiality law, from detailing disciplinary actions other than to the student involved or that child’s parent.

The headmaster called it “deplorable’’ and “unconscionable’’ that anyone would make public an incident involving a minor that was addressed long ago and resolved.

“This is an old allegation that is well more than a year old. It had nothing to do with my actions in resigning,’’ she said.

“I find this completely outrageous,’’ she added.

The incident occurred in March 2015. It included an alleged racial slight and evolving into alleged cyberbullying against a white student.

The accused student had allegedly posted a caricature in blackface on a group chat and likened it to an African-American classmate at Boston Latin. When a white friend defended the classmate, she was harassed by the student and four other friends in text messages and on Instagram, the parents of the girl told the Globe Friday night.

The parents said Teta spoke with them about the case, despite her personal tie to the student. Their daughter continued to be bullied by another student who was never effectively disciplined, they said.

The School Department’s Office of Equity had been ­reexamining the case in recent months, and the parents met with Superintendent Tommy Chang several months ago, they said.

Four days before Teta resigned, the Office of Equity informed them that the school had mishandled the case, the parents said.

The new development caps a tumultuous year at the school. Just this week, Teta submitted her resignation and assistant headmaster Malcolm Flynn, who has been at the school for 52 years, announced that he, too, would step down.

The school has been embroiled in controversy since January, after two students posted a YouTube video describing unchecked racial incidents at the school. They also held a meeting at the school urging other students to share their experiences. And they invited others to post their stories on Twitter.

The video prompted calls by civil rights activists for Teta to step down. A federal investigation was launched, and the equity office began a probe.

The equity office returned its findings in February, saying school administrators acted properly in all but one of seven cases they reviewed. The investigation covered every alleged incident involving racial or ethnic bias reported to Boston Latin School administrators that occurred between November 2014 and January 2016, said Richard Weir, the school department’s communications chief.

Since then, the Office of Equity received and investigated 105 reports regarding racial or ethnic bias at Latin School, including five alleging insufficient action by administrators, he said.

In her resignation letter, Teta said she was stepping down with a “heavy heart’’ because it was the right thing to do for the school.

“My resignation is predicated on the hope that by removing myself, the climate of tension that has permeated the school will dissipate and the focus of BLS will return to the incredibly demanding work at hand,’’ Teta wrote.

She also expressed her frustration that the school and its efforts to combat racism “have been unfairly judged’’ by others beyond the school’s walls.

Meghan E. Irons can be reached at meghan.irons@globe.com. Follow her on Twitter @meghanirons.