Bail for James and Jennifer Crumbley, aged 45 and 43, was set at $ 500,000 each in a virtual arraignment hearing.
The couple were also told they could each face up to 15 years behind bars.
Ms Crumbley cried as she told Judge Julie Nicholson that she understood the charges.
Their son Ethan Crumbley, 15, is accused of opening fire at Oxford high school Tuesday in an outburst that left four dead and eight injured.
Mr. and Mrs. Crumbley are accused of having bought their son the handgun used in the shooting.
They are also accused of ignoring signage before their son’s rampage, like a drawing found on his school desk with the words “blood everywhere” on it.
The couple had disappeared hours after the charges were announced and were eventually found in a commercial building where they “appeared to be in hiding”.
A subsequent statement from the couple’s lawyers denied they were on the run and claimed they were returning to the area after leaving “for their own safety” on the night of the shooting.
Oakland County Prosecutor Karen McDonald said the parents had committed “serious” acts, ranging from buying a gun on Black Friday and making it available to their teenage son, resistance to his withdrawal from school when they were summoned a few hours before the shooting.
Investigators said the gun was legally purchased by Mr Crumbley last week – apparently as a Christmas present – and was “freely available” to the teenager.
Ethan reportedly posted images of the gun used in the shooting to social media, writing, “I just had my new beauty today” and adding a heart emoji, the Oakland County prosecutor said , Karen McDonald.
Ms Crumbley posted the next day that they were “testing her new Christmas present”.
School officials had become concerned after a teacher once saw the teenager searching his phone for ammunition during class, Ms McDonald said.
Yet when Ms. Crumbley was contacted, she told her son in a text message, “Lol. I’m not mad at you. You have to learn not to get caught. “
The victims of the shooting are Tate Myre, 16, Hana St Juliana, 14, Madisyn Baldwin, 17, and Justin Shilling, 17.
Crumbley’s parents were called to the school on the day of the shooting “for worrying behavior in the classroom”.
The shooting took place a few hours later.
Crumbley entered a bathroom with a backpack and came out with a semi-automatic handgun, shooting the students as he moved down the hall.