The International Rescue Committee (IRC) said unless interventions are "urgently funded", the humanitarian needs of children will only increase.
"Education in emergencies is a life-saving and life-changing intervention - helping children recover and cope with the continuing adversity they face," said Sarah Smith, the IRC's senior director for education, on Friday.
"This is incredibly urgent for Rohingya children; no one is paying attention to their needs, and they face some of the highest levels of trauma the IRC has ever seen.
"Until children's rights to education in the Rohingya crisis are realized, we face the threat of a lost generation of what is already one of the world's most vulnerable populations."
Less than two percent of humanitarian funding goes towards education, the most underfunded sector in response to the Rohingya plight, the IRC said.
Evan Schuurman, part of the Save the Children's emergency response team in Cox's Bazar, said in October that schooling was particularly important for traumatized refugee children.
"School isn't just about learning," he wrote in a piece published by Al Jazeera. "It provides routine and a sense of normality, a place where children can make friends, play and remember what it's like to be children.
"It's also a critical form of protection from exploitation and abuse, such as trafficking."
According to the Oxford Burma Alliance, a student-run organization at Oxford University, more than 60 percent of Rohingya children between the ages of five and 17 have never been to school due to poverty, government restrictions on their movement, and a lack of schools in Rakhine State, Myanmar.
More than 620,000 Rohingya have fled to neighboring Bangladesh since August 25 in fear of abuses by Myanmarese soldiers, which UN described as "ethnic cleansing".
The ongoing crisis has been described as the biggest forced exodus of 2017.
Bangladesh and Myanmar signed a deal last month for the return of hundreds of thousands of Rohingya refugees, but little is known of its details.