PALO ALTO -- Saying that he needed to take a break, Superintendent Kevin Skelly sent an email to parents and community members on Tuesday, informing them that he will resign at the end of the school year from the Palo Alto Unified School District.

Skelly, 53, who has weathered successive controversies in the K-12 district, wrote that he wants to spend more time with loved ones and contemplate on his next move. He said Tuesday that he probably will not stay in Palo Alto and that he could again work as superintendent for another district. But for now, he said, he plans to take time off: "Perhaps this next school year is the gap year I never had," he said, referring to the yearlong break that some students take between high school and college.

The decision was entirely his, both Skelly and board President Barb Mitchell said. He has two years remaining on his contract, which after a 3 percent one-time bonus this year pays him about $300,000 annually.

Mitchell said that she was sad about Skelly's decision to leave. "He's a very popular superintendent. We will miss him, and we all have benefited from the contributions he made."

In June, Skelly will have led the district for seven years, the second-longest tenure of a Palo Alto schools superintendent in 40 years.

While contentious debate is not unusual in Palo Alto, in recent years the district was the target of investigations by the federal Department of Education's Office for Civil Rights, over the handling of students' bullying complaints. That controversy continued as the administration and board wrestled to create a policy to combat bullying; most recently they angered teachers in dismissing a proposal to eliminate tracking in freshman English classes at Palo Alto High.

Parent Ken Dauber, a frequent critic of the district, credited Skelly for important contributions, in particular shepherding through a plan to ensure that all students graduate with credits required for admission to California's public universities, known as the A-to-G requirements.

Dauber said the he hoped Skelly's departure would offer an opportunity to reconsider values. "Those should include a concern for academic achievement and also for students' social-emotional well-being and making sure that all students in the district get an equal opportunity to succeed."

Skelly will step down June 30. He said that seven years is a good point to take a break, just as the youngest of his four children is graduating from high school. He said he'd like to take a cross-country trip -- his parents live back East -- and spend more time with his wife Carrie.

The furious debates of recent months did not prompt him to resign, Skelly said. In Palo Alto's intensely involved and vocal community, "Predecessors told me that this was one of the most demanding placed to be a superintendent," he said. "It is."

Mitchell agreed. "It's a tough community for a superintendent." The board set 64 goals in its strategic plan; in addition, parents, employees and various interests place demands on schools. She said that Palo Alto needs to do some soul searching, in its expectations of its leaders.

Skelly, she said, listened well to various viewpoints. "He worked really hard to come up with solutions and options that represent common interests."

Skelly was hired in 2007, and was welcomed as a calming leader after the tumultuous tenure of former Superintendent Mary Frances Callan, who so incited district managers that they called for her resignation.

There is no indication that the board has been unhappy with Skelly. Mitchell noted that the school board extended his contract to the four-year legal maximum term every year during his superintendency, except when he requested otherwise. It was not lengthened last spring.

The board, Mitchell said, will seek community input into what qualities its next school leader should have.

Dauber said he hopes the board conducts the search for its next superintendent "with full transparency and participation from the whole community."

Contact Sharon Noguchi at 408-271-3775. Follow her at Twitter.com/NoguchiOnK12.