[1][2] The son of William Paynter or Cambourne, from Antron in Sithney, and Jane, the sixth child of Richard Keigwin of Mousehole, he was born at Trelissick Manor in the parish of St Erth, Cornwall, England, and baptised on 7 December 1637.
The same year he faced scandal when a child was left on his doorstep in college and was claimed to be his; it was later revealed that John Jago, a disaffected undergraduate expelled by Paynter for debauchery, had tried to wreak revenge.
On 15 August 1690, Paynter was elected by a depleted Fellowship to the Rectorship of Exeter College, on the deprivation of Arthur Bury.
The Exeter fellowship was divided by the decision of the Bench; both Bury's opponents and his supporters attempted to run the college.
The resulting disorder was not put right until 1694, when the House of Lords confirmed Paynter as rector after reversing the decision of the King's Bench.