The checks, written between early September and early November 2013, transferred money from the foundation's Charles Schwab account into a JP Morgan Chase account at an unknown location, deputies said.
"It is so disheartening that a crime such as this has been perpetrated against the Foundation," said Superintendent Lisa Gonzales in an emailed statement. "I am confident that the authorities will soon identify the person or persons responsible, and that the investigation will bring all relevant details to light very soon."
The foundation has not yet responded to a request for an interview.
The checks were written out to "Eye For Design LLC" with a mailing address in Monroe, Connecticut, deputies said.
The incident has a reporting date of Nov. 25. The Sheriff's Office typically issues crime reports on a weekly basis; an incomplete report on an individual case can delay publication.
The checks were pre-printed with the foundation's name misspelled and without the foundation's address, but did include the correct account and routing numbers on the bottom of the checks, deputies said.
Investigators from Charles Schwab and U.S. Postal Police are working on the case, deputies said.
The news comes as the Portola Valley School District is in the midst of recovering from an embezzlement of nearly $101,000 by former superintendent Tim Hanretty, who is serving a two-year term in state prison.
When the cost of the investigation into his crimes is included, Mr. Hanretty's actions set the district back by $182,000, nearly $121,000 of which he had repaid, according to an Almanac report in September.
"The many volunteers of the Portola Valley Schools Foundation have worked tirelessly for almost two decades in support of the students and staff at Ormondale and Corte Madera Schools," Ms. Gonzales said in her email. "Especially over the past two challenging years, the support of the foundation has been instrumental in ensuring that key programs and staffing levels have continued uninterrupted, and our students have received the best education possible."