Michael Pepper, the man trying to reshape the organisation famously dubbed "Neanderthal" by former education secretary John Patten, is due to leave his job today. This is the second sudden exit from the body which claims to represent home-school associations in 12,000 schools.
Six years ago Phil Woods, its general manager, was dismissed after a weekend meeting of the NCPTA's executive committee.
Mr Woods, appointed to raise the group's profile at a time when the Government was seeking more parental involvement in schools, had been in post for just a year.
Mr Pepper, a former project leader with the Benefits Agency in York, would not comment this week on his resignation.
But Ian Price, NCPTA chairman, said: "The chief executive has tendered his resignation and he leaves formally on Friday having been with us for three months.
"He has been a positive influence for development, but unfortunately felt it was necessary to withdraw before seeing it reach fruition."
He had been undertaking a thorough audit of the 40-year-old organisation with a view to producing a strategic plan to take it into the next century.
There are moves within the organisation for it to adopt a regional structure, with supporters arguing this would increase accountability and membership.
Mr Pepper also had the tricky job of liaising between the 15 trustees, who establish policy at national level for the NCPTA, and the six-strong staff who implement it.
His resignation comes at a time when the organisation, which has always insisted that it is apolitical, may be embroiled in more politics. For Sean Rogers, a Labour activist once suspended as a councillor in Trafford by the national party, is set to become chairman next year.