David Hawker, director of children's services at Brighton and Hove Council, was the National Association of Headteachers' candidate to replace David Hart as general secretary.
But, in a two-horse race, Hawker received only a third of the votes cast.
Some 4,374 members voted for Hawker while 8,863 voted for rival Mick Brookes, head of Sherwood Junior School in Nottingham.
The union's president, Rona Tutt, said the result showed many heads were "a little bit apprehensive" about working more closely with children's services.
"I don't think there's any doubt that our members embrace the Government's agenda but what they are concerned about is the rate at which things are changing," she added.
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