A second half equaliser by Richard Kell ruined Colin Calderwood's first home game in charge of Northampton Town.
Calderwood saw his side dominate the first half and create a wealth of chances. But they only had Martin Smith's stunning 25-yard free-kick in the ninth minute to show for their efforts.
And the Iron made them pay for wasted chances, by deservedly grabbing a share of the spoils when Kell's 52nd minute shot deflected off the heel of Chris Willmott and looped over Lee Harper in the home goal.
Northampton's performance tailed off the longer the game went on, with the visitors the likelier winners.
Indeed, it took a brilliant diving save from Harper to deny Steve Torpey in the 62nd minute, while Paul Trollope's defensive header five minutes later came back off the crossbar.
It had been a different story before the break as the Cobblers pressed to cash in on their early lead, and Smith headed wide from a Paul Harsley free-kick and was inches away from converting a Josh Low cross.
Smith's strike partner Marc Richards also had his chances, bursting clear in the 19th minute only to fire wide and heading against the crossbar four minutes later from a Chris Carruthers cross.
Richards raced onto a Smith pass after half an hour only to see Sam Russell save with his legs while at the other end Steven MacLean had a clear shooting chance three minutes before the break but volleyed straight at Harper.
Scunthorpe felt they should have had a penalty in first half stoppage time when Ian Sampson brought down Torpey but referee Lee Cable awarded a free-kick inside the D and Lee Featherstone's shot was deflected wide.
Iron boss Brian Laws said: "I was disappointed in the second half that we didn't go on and win the game.
"We have had so many injuries lately that when Matthew Sparrow went off in the first half with a calf injury the players could have been excused for packing it in but they came out in the second half and showed tremendous spirit."