The Fairfax County Board of Supervisors appointed Kohann H. Whitney, a longtime political aide to Supervisor Martha V. Pennino, to a two-year term on the County School Board yesterday.

Whitney, business development manager for the County Economic Development Authority, will replace Carmin C. (Chuck) Caputo, whose second full term expires July 1. Caputo was named to the School Board by Pennino to represent her Centreville District in 1980.

Pennino, a Democrat who is vice chairman of the Board of Supervisors, asked her fellow supervisors to replace Caputo, saying "It's been my custom to rotate the appointment." She said she has named five School Board members in her 17 years as a supervisor.

Caputo, she said, "is not being dumped or ousted. He has served with distinction. I have no quarrel with him."

But she said a factor in her decision not to reappoint Caputo was his failure to file required financial disclosure forms on time. That failure was cited in a lawsuit by parents opposed to the School Board's decision to close Fort Hunt High School.

Caputo, who voted to close Fort Hunt, has said he did not realize he missed the deadline.

Some observers questioned whether Pennino's decision not to reappoint Caputo stemmed partly from active support by Caputo's wife, Barbara, for Gerald L. Baliles in the recent Democratic gubernatorial caucuses. Pennino, who supported Baliles' opponent, Lt. Gov. Richard J. Davis, said that was "irrelevant."

Whitney, 40, was Pennino's assistant from 1976 until last year, when she went to work for the Economic Development Authority, which encourages business to locate in Fairfax County. She also is Pennino's appointee to the County Library Board of Trustees.

She has served on several school bond referendum campaign committees, has a son in eighth grade and has been a Fairfax County PTA member since 1976.

She said in a telephone interview after her appointment that "Fairfax County has an excellent school system. To be able to be a part of that will be very exciting."

Whitney's appointment is the latest in a series of high-level changes in the Fairfax County schools. She will join the 10-member School Board at the same time as Frank Francois, named by the supervisors last month to replace Robert E. Frye. The system also is acquiring a new superintendent, two new deputy superintendents and at least one area superintendent this summer.

School Board member Laura I. McDowall, when asked whether the number of changes could threaten continuity in the region's largest school system, said, "It does lead to anxiety, but I have a lot of confidence in the system."

Pennino said after the vote, "There's no need for continuity on the School Board."

Caputo issued a statement that said in part: "I am disappointed, of course, but I am also grateful to have had the rewarding experiences of the past five years and the rare opportunity to influence education in this outstanding system."

Pennino's method of selecting her School Board member without forming a selection panel or holding public hearings drew criticism from one civic activist. Linda A. Singer, a founder of the Reston PTA-PTO Council, said Whitney is "extremely competent," but "there should have been a panel."