The Reach Academy for Girls charter school will be closing.
But Delaware Secretary Education Mark Murphy and the State Board of Education allowed Gateway Lab School to stay open but will be required to improve its test scores or face closure.
Meanwhile, Murphy delayed a decision on Family Foundations Academy.
He said that there were serious allegations of financial mismanagement that have arisen over the last few days.
The Education Secretary said regulators needed time to review them before acting.
Reach Academy was the only all-girls public school with around 380 students while Gateway serves students with disabilities, behavior issues and other problems.
It has an enrollment of 210 students.