September 11 impacted Mon Don and other high schools across the country. While no MDHS students or their immediate relatives died in the attacks, Mon Don experienced several changes in their aftermath.

Flights 11 and 175 crashed into the World Trade Center during the first period (before 9:25). The South Tower (hit by 175) collapsed, followed by the North Tower, during the second period of classes. Other incidents occurred in Pennsylvania and Arlington, Virginia (at the Pentagon) during the second period (after 9:30 and before Flex). During Flex, many students crowded into the Quad to discuss what had happened. While school was not officially cancelled that day, hundreds of students received permission to leave early. A prayer service was held in the afternoon in the church. Building 7, another skyscraper in the World Trade Center complex, collapsed three hours after the school day ended, although it was not hit by a plane. Mon Don remained open the next day; few schools in New Jersey were closed on Wednesday, September 12.


Security cameras were installed in some locations on campus, the breezeway was closed, and students were required to wear their ID's on lanyards by the beginning of the next year (2002-2003). In 2004, students were required to wear uniform shoes, despite most students signing a petition against it.

In 2002 and 2003, on the first and second anniversaries of the attacks, all students gathered on the track for a short prayer service. Several years later, a "peace pole" was installed in the Quad, with messages of peace in English, Hebrew, and Arabic.