As police confronted armed attackers who blasted guns through the streets, students and teachers were forced to hunker down while the shootout was happening blocks away.
Officials said all of the city's 30,000 students in 43 schools were accounted for and safe.
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Among those locked down were students at Sacred Heart School, a pre-K through 8th grade Catholic school on Bayview Avenue near the shooting scene.
There was a delayed opening Wednesday and plenty of parents did return their kids to school, but students were still shaken up.
The district superintendent is proud that no one was hurt and the schools were not compromised during the incident, but now the district wants to be even more prepared moving forward.
"Lockdown is the new normal," Superintendent Franklin Walker said. "Lockdown is something we do on a regular basis, it's very frightening, it's very scary, you know all sorts of things go through the minds of children and adults when these kinds of things happen, but unfortunately, at this point in time, at this day in age, it's a practice that's necessary."
Counselors will be available for students and their families if need be.
Six people, including a police officer and two suspects, were killed in the shootout.
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Jersey City Mayor Steven Fulop said Wednesday morning that the gunmen targeted the market, with surveillance video showing them driving slowly through the city's streets before stopping outside, calmly exiting their van and immediately opening fire.
New Jersey authorities are preliminarily investigating the incident as a case of domestic terrorism.
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