The two boys are aged 16 and 17 and managed to force their way out of the locked building in which they were accommodated by holding a sharp implement at the throat of the female staff member.
Whether she was forced to unlock the door or whether they managed to force it open is not yet clear.
The woman was released by the teenagers a short distance from the Sirius treatment centre. The boys fled the scene and remain on the loose on Sunday morning.
According to Kenneth Sundin at Uppsala police the woman escaped unscathed but for a small cut on her throat.
Police deployed search dogs during the night to look for the teenagers, but the search has now been called off.
“We do not have anything specific at the moment as we do not know we should look. We have no search zone,” Per-Erik Eriksson at Uppsala police to news agency TT.