Maija Neilande has stepped down and will leave the post from August 1, according to Irēna Škutāne, a local councilwoman who heads an investigative committee responsible for reviewing the allegations of abuse.
The orphanage has been tasked with improving conditions for the children staying there.
A total six caretakers have left the orphanage in light of the findings. One was fined for abusing a child staying there.
As reported previously, experts sent to examine the Jelgava City Orphanage for the upcoming deinstitutionalization project alleged witnessing several episodes of abusive behavior by the staff.
"What I experienced was hell ... adults and support personnel no longer control neither their emotions, nor their actions," had said psychologist Andrija Likova, one of the people sent to review the institution.
Latvia's child protection authorities have started three cases, of which one has since been closed, in light of the findings.