The Superintendent confirmed it was a lockdown and not a shelter in place.
Police told Ruskin Elementary School and St. Victor School to go on lockdown soon after officers were dispatched to a report of a burglary in progress on nearby Zion Lane at about 9:50 a.m., police spokesman Officer Albert Morales said.
The lockdowns were lifted at about 12:40 p.m. after officers arrested the burglary suspect, Morales said.
"We're satisfied we have the person we're looking for," Morales said, adding that police were still in the process of identifying the suspect.
The suspect did not appear to have a firearm, Morales said.
Kialyn Higashi, school secretary at Ruskin, a K-5 public school at 1401 Turlock Lane, said the school was told by police to "shelter in place" shortly before 10:30 a.m., and got the all-clear notification at about 12:47 p.m.
"Students were fed their lunches" in their classrooms, Higashi said. "They remained in the building until it was lifted."
"There have been a lot of robberies here in the Berryessa area," Higashi added.
St. Victor's is a K-8 private Catholic school at 3150 Sierra Road.