Parkin came off the bench to squeeze a left foot shot under Exeter keeper Artur Krysiak, who had earlier denied the home side with a string of fine saves.
The 76th-minute goal stretched Scunthorpe's unbeaten run to nine games and left the Grecians deep in relegation trouble after seven defeats in their last nine games.
The visitors, who made five changes to try and halt that slide, might have snatched an early lead but striker Lauri Dalla Valle headed straight at goalkeeper Sam Slocombe from close range.
A strike then might have made a real difference, but after a goalless first half, Scunthorpe who picked up the tempo in the second.
Midfield man Josh Waler and young Everton loanee Conor McAleny were both denied by the woodwork as Exeter were stretched at the back.
Krysiak also came to Exeter's rescue with good saves to deny McAleny and Jimmy Ryan.
Exeter battled hard and long range efforts from David Noble and Liamk Sercombe tested Slocombe before Parkin settled it with the sixth goal of his loan spell from Championship side Cardiff City.