But her departure is one of a four high-level administrators, whose replacement will result in a new leadership team for the district and possibly result in merging supervision of elementary and secondary schools into one K-12 position.
Skelly told the Board of Education this week that new hiring will be one of his most urgent goals for second semester.
"That work is going to take a tremendous amount of time on the part of the senior cabinet and the board. In this organization, people are the most important part of our work," he said.
McEvoy, whose three-year tenure was marked by improved student achievement as well as by rocky relationships with some parents and students, said she was resigning for personal reasons "with a bittersweet heart."
She previously served seven years as principal of San Mateo High School.
In a letter to the Paly community, she expressed gratitude for the "powerful work" being done at the school and stated her pride in the school's constant push for excellence.
While some students and parents praised her no-nonsense approach to the job, others criticized McEvoy throughout her tenure for what they called her "punitive" discipline style and unilateral decision making.
When she arrived at Paly, she directed teachers to strictly enforce an attendance policy to discourage students from cutting class; she changed how schedule changes could be made, favoring parental approval; and she expected a policy against sexually suggestive dancing be enforced at school dances.
In 2007, a conflict between McEvoy and history instructor Mike McGovern, who used to mount student-run historical re-enactments, riled students.
Most recently, her handling of suspensions following an Oct. 27 egg fight between Paly juniors and seniors drew both ire and praise. After imposing five-day suspensions, McEvoy reduced them to one-day suspensions and said she would expunge them entirely if students stay on good behavior for the rest of the year.
Palo Alto lawyer William D. Ross then threatened the Board of Education with a lawsuit if it fails to expunge the suspensions immediately, saying the discipline record would unfairly interfere with students' ability to win athletic scholarships.
Last week, Skelly thanked McEvoy for her leadership at Paly.
"Under Dr. McEvoy's leadership, numerous measures of school success improved, including California standard-test results, SAT scores and Advanced Placement test participation," Skelly said.
"Dr. McEvoy also led the school through a successful accreditation process and the completion of the school's master plan for facility improvements.
"I want to thank Jacquie for all her efforts on behalf of (Palo Alto Unified School District) children, youth and families over the last two-and-a-half years and wish her the best in her future endeavors," he said.
Skelly said he has yet to decide on the composition of a search committee but wants to begin immediately in competing for top talent. He said the search process would solicit input from teachers and students.
McEvoy's departure coincides with other high-level exits from the school district, leaving Skelly with an opportunity to reshape his leadership team.
Many of those retiring or resigning had served many years in Palo Alto, he noted.
"We're a relatively new team, and it's a lot of change," said Skelly, who is finishing his third year with the district. "We want to make sure we keep some historical knowledge within the organization.
"Finding quality individuals is one of the most important things we can do to strengthen the organization. Other districts are out there looking for candidates, too," he said Wednesday.
He is advertising nationally to replace Carol Zepecki, director of special education and student services, a 12-year district veteran, and Linda Common, assistant superintendent of administrative services, a former Woodside High School principal who joined the district just last summer.
Secondary Director Burton Cohen will retire in June, and Elementary Director Becki Cohn-Vargas has not been replaced since resigning last fall.
Skelly said he may combine the directorships of elementary and secondary education into a single position, director of K-12 education.