Pools took command with two goals in 17 first-half minutes to stretch their unbeaten run to six games.
James Poole fired the visitors in front after 20 minutes, lashing home a shot from 12 yards out after a good lay-off by Charlie Wyke.
They struck again in the 37th minute when midfielder Jonathan Franks waltzed his way into the box before steering an excellent left-foot shot into the far corner of the net beyond the outstretched arm of goalkeeper Sam Slocombe.
Scunthorpe, who had won their previous three home games, struggled to get a foothold in the match and in the second half it was Hartlepool who continued to threaten on the break.
The lively Poole rattled the crossbar with one long range effort - then tested Slocombe with another.
With 67 minutes gone, Scunthorpe gave a debut up front to new loan signing James Alabi from Stoke.
Nine minutes later he made a real impact, heading them back into the game from a left-wing cross from Tom Newey.
But it was too little, too late to save Scunthorpe from an eighth home defeat of the season.