Manager Nigel Adkins named an attacking line-up for the game, with Ben May and Hooper starting up-front. Josh Lillis deputised for the injured Joe Murphy, whilst the defence consisted of Cliff Byrne, Izzy Iriekpen, Kenny Milne and Marcus Williams.
Grant McCann partnered Ian Morris in the centre of midfield, whilst Kevan Hurst and Jonathan Forte took their places on the wings.
Scunthorpe started the game brightly, but suffered an early blow when Ben May hobbled off after just eight minutes. Paul Hayes replaced him up-front.
New signing Gary Hooper was showing some good touches, and had the first shot of the game with 34 minutes gone. However, his volley flew over from 20-yards out.
Two minutes later, the Iron were in front.
Izzy Iriekpen's looping header from Grant McCann's corner caught the Town keeper Phil Barnes out and nestled in the back of the net.
Scunthorpe continued their pressure in the second half, Kevan Hurst went close just after the restart, but his effort fizzed narrowly over.
United doubled the lead on 54 minutes, when Gary Hooper calmly chipped the ball over Barnes following Paul Hayes' throughball, to earn his first goal in Iron colours.
The pressure continued to mount on Grimsby, and they found themselves three goals down 10 minutes later, when Hooper notched his second of the match with a back-post header.
Cliff Byrne could have made it four, but his effort was well saved by Barnes.
The win was sealed with 10 minutes remaining, when Jonathan Forte drilled in a low shot from 20-yards out.
A crowd of 1,644 spectated United's 18th Lincolnshire Senior Cup victory.