Buffeted for the past several years by critics who charged that his leadership lacked transparency, Skelly said he had informed the Board of Education of his decision Feb. 11.
"Seven years is a long time to be superintendent in Palo Alto, and it's the right time for me to go," Skelly said Wednesday, adding that he expects to be a superintendent again in another school district but has no immediate plans. "I like the work — I really like the work."
Board of Education President Barb Mitchell said that, while the resignation was not a complete surprise, "The decision was entirely Dr. Skelly's.
"The board feels a deep sense of respect and gratitude for Dr. Skelly's leadership over the past six and a half years," Mitchell said, citing his "personal integrity, devotion to students and the durable improvements he initiated and facilitated to benefit all current and future students."
She said the board would discuss a process and timeline for a search for a new superintendent at its meeting on Tuesday, Feb. 25.
Skelly's seven-year tenure in the job is slightly longer than average for a Palo Alto superintendent in the past 70 years. The most recent superintendent to serve longer was Newman Walker, who served for a decade, from 1975 to 1985.
"I have so enjoyed working with students, parents, staff and the school board to create the best possible environment for students to learn and grow," Skelly said in an email to families and staff.
"The sense of collaboration and commitment to serving students better that I see in so many people has been a source of continuous inspiration."
Skelly has overseen a massive building boom to modernize and expand capacity on Palo Alto's 17 campuses, funded by the $378 million "Strong Schools" bond measure passed in 2008.
Under his watch, the district stiffened high school graduation requirements in an effort to boost expectations for minority and low-income students, many of whom historically have graduated with less rigorous courseloads.
Skelly has advocated giving principals wide rein to run their campuses and built a system-wide professional-development program to serve the district's 800-plus teachers.
His tenure saw the much-debated adoption of the K-5 math curriculum Everyday Mathematics and a controversial change in the district-wide calendar to end the first semester before the December holidays — an effort to give work-weary high school students a clean break.
A former teacher, Skelly commutes around town by bicycle, plays basketball with students and clearly delights in their accomplishments, academic and otherwise.
In a survey last year, 90 percent of Palo Alto parents and 93 percent of high school students said they were "somewhat satisfied" or "very satisfied" with the education children receive in the school district, which routinely ranks among the highest-scoring in the state.
"I was very sorry to hear that Kevin Skelly has decided to leave in June," said Teri Baldwin, president of the Palo Alto Educators Association, the teachers' collective-bargaining group.
"He has always had an open door policy for me to come in and discuss concerns, and he worked with me to help solve them.
"In all of our discussions it was clear that Kevin is passionate about education. He is very pro-teacher and that can be hard to find. A good district is built upon its teachers, and Kevin understood that."
Sigrid Pinsky, president of the Palo Alto Council of PTAs, said Skelly had been accessible and eager to hear parent concerns. She cited his execution of the district's strategic plan, fiscal management skills and support for Project Safety Net, a community coalition to promote well-being that formed in the wake of student suicides in 2009 and 2010.
"Kevin has demonstrated his commitment to the academic and social emotional health of all of our students," Pinsky said. "He has been tireless in his work and maintains his sense of humor throughout."
But Skelly was widely criticized last year for failing to promptly disclose a December 2012 finding by a federal civil rights agency that the district's mishandling of a middle school bullying case had violated the civil rights of a disabled student.
The district has spent more than a year trying to revise its policies and procedures in response to that finding.
After the federal finding, several other families filed complaints against the district with the U.S. Department of Education's Office for Civil Rights (OCR).
One of those remains pending, while three have been resolved in the district's favor or dropped for lack of evidence. An additional investigation — initiated last year by the federal agency itself and pertaining to the district's compliance with Title IX, which bars sex discrimination in education programs receiving federal funds — also remains pending. Two other cases filed prior to the December 2012 finding have been closed.
Parent Christina Schmidt, chair of the Palo Alto Advisory Committee for Special Education, said Skelly had been supportive of the group's activities and was able to "connect with many people, especially students, and earned the respect of his district staff.
"Nonetheless, Dr. Skelly's best efforts were simply not enough, and his missteps were the primary reason for the community's criticism about the OCR investigations and the subsequent development of policies," Schmidt said.
"We believe that Dr. Skelly came to understand that the district needed a change and sometimes we must be the catalyst for change even if it means stepping aside."
Schmidt said candidates to replace Skelly should have "a track record of supporting students with learning differences and special needs" and an appreciation for "transparency and community input."
Skelly also has come under persistent criticism by a parent group called We Can Do Better Palo Alto, which has pushed district officials to compel major reforms to the counseling program at Gunn High School and to impose firmer rules to curb homework and to coordinate the number of tests or papers a student can have in a given week.
Ken Dauber, a cofounder of that group and an unsuccessful candidate for school board in 2012, said Skelly's most significant contribution has been changing the high school graduation requirements "to try to ensure that all of our students graduate ready for college.
"The superintendent selection process is an opportunity for the community to renew our traditional focus in Palo Alto on providing a quality education that challenges and supports the whole student, including academic achievement and social and emotional well-being," Dauber said.
Marielena Gaona Mendoza, a former district parent who maintains that minority, low-income and special-education children routinely face stereotyping and discrimination by school personnel, called Skelly's resignation "news that we were longing for, and it finally happened.
"Hopefully the next super is not afraid to talk to the principals and let them know when they are failing our kids and improve our counseling system and special education for Latino students," Mendoza said.
Skelly, who began his career as a math teacher and moved up the administrative ranks, arrived from southern California to become superintendent in 2007. In 2012, the school board extended his contract until June 2016.
The board did not give Skelly a raise last year but did award him a 3 percent, one-time bonus on top of his regular pay of $287,163.
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