More than $7,000 raised by students vanished at a Harlem elementary school and the city is probing where the missing dough went and why it was never reported by the principal.

Parents at PS 36 raised $13,625 last school year for class trips and graduation festivities. But PTA vice president Valencia Moore said the group’s books, kept by PTA president Keisha Cole, did not reflect the amount of money taken in during three fund-raisers in November 2014 and spent on annual class pictures.

Other parents said they did not get refunds of hundreds of dollars for a canceled class trip to Connecticut.

Moore and other parents pressed principal Heather Jn Baptist to meet with Cole and address the discrepancies, according to June 9 ­e-mails obtained by The Post. But when she took no action, parents said, they reached out to city officials.

“I know the principal is fond of Ms. Cole and doesn’t want to believe that she could do something,” Moore said via e-mail. “I would hate to think the principal doesn’t want an investigation because she, as well, has something to hide.”

Cole fired back that such insinuations were a “pack of lies” and blamed a former president for embezzling nearly $8,000 two years ago.

“I didn’t take any money from anybody,” Cole told The Post. “If anything I took money out of my own pocket to help the kids.”

Jn Baptist did not return messages seeking comment.

Department of Education officials confirmed they are probing Jn Baptist for failing to report the alleged misuse of school funds.

“Any school-sponsored fund-raising must only be used to support school programs,” said spokesman Harry Hartfield.