Nagle, who is finishing his third year as principal of the 415-student K-5 campus, broke the news in an email to parents and staff Tuesday afternoon.
The announcement followed tensions at the school apparently precipitated by Nagle's controversial recommendation not to renew the contract of a popular school librarian. The dispute led other staff members, with support from a number of parents, to come forward with complaints, sources said.
In his email, Nagle said he had "nothing but gratitude" for his three years as principal at the school.
"I know that the district will find another principal talented enough to lead this school into the next year and beyond."
Nagle was hired to lead Juana Briones in August 2009, replacing principal Michael O'Neill, who resigned in late July after two years at the school to take a job on the East Coast.
Nagle had been an elementary school principal for seven years, having previously served at Blackford Elementary School in San Jose and Marshall Lane Elementary School in Saratoga.