Student protests have continued at one of New York’s premier college preparatory schools after an assistant athletic director made a derogatory comment to a 16-year-old African American student-athlete that caused him to withdraw from the Roman Catholic-headed academy.

Tony Humphrey, a standout baseball player at Iona Preparatory School who already has committed to play collegiately at Boston College, said that now-former assistant athletic director Bernard Mahoney questioned why Humphrey decided to run on the track team.

“[Mahoney] said ‘it never hurts to gain speed,’” Humphrey recalled.

“But he said I was already fast enough because I gained that speed by running from the police.”

When Humphrey told his mother, she immediately withdrew him from the school.

Alex Malecki, a spokesman for the school located in the New Rochelle section of Westchester County, said the assistant resigned.

Thomas R. Leto, the president of the private school run by the Edmund Rice Christian Brothers, said Iona doesn’t condone the assistant’s behavior.

Such comments “go against the very mission of the school to develop “moral and ethical leaders, as well as the Essential Element of an Edmund Rice Christian Brother Education to celebrate the value and dignity of each person,” Leto said in the statement.

“It is behavior that Iona Preparatory does not condone for its students and will not accept from its faculty and staff.

With about 750 students and a population breakdown of about 68 percent white and 12 percent African American, Leto asserted that one of the most critical aspects of Iona Prep remains the acceptance and respect of every student.

“[That aspect] has been infringed upon,” Leto insisted in the statement.

“On behalf of the administration and staff, I am deeply sorry to this student and those most offended and negatively impacted.”

Leto said the school immediately began investigating the incident after it occurred.

He noted that he addressed friends and classmates of Humphrey who staged a walkout in protest of the racially insensitive remarks.

“Despite all we have undertaken, including a recent three-week respect campaign, there is much work to be done, as such conduct and comments cannot be tolerated any longer,” Leto insisted.

“We remain fully committed to being an open, welcoming, embracing, and nurturing community, where every young man holds a special place in the brotherhood of Iona men.”

Humphrey told reporters that it wasn’t the first time he found himself on the receiving end of racist attacks at Iona Prep.

“During my freshman year, I took it up with the deans, I too it up with the higher-ups, and nothing happened,” Humphrey asserted.