Scunthorpe, improving fast after relegation from the Championship and a slow start to the season, were given a great start by Martyn Woolford.
The former York midfielder celebrated his first league start for the club with a goal after four minutes, slotting in a low cross from Paul Hayes from close range.
Brighton fought back from that early set-back and Joe Murphy saved well from Glenn Murray and a Dean Cox header.
Hooper doubled United's lead in first-half stoppage time. The Brighton defence froze thinking the ball had gone out of play and Hooper easily stepped inside Colin Hawkins before finding the far corner.
The home team's hopes of a second-half revival were destroyed in the 55th minute when Matt Richards inadvertently headed the ball back into the path of Hooper.
He held off David Livermore to beat Michels Kuipers with an angled right-foot drive which the Dutch keeper got a hand to but could not keep out.
Murray should have pulled a goal back for Brighton ten minutes later but poked wide of the far post with the outside of his right foot.
Hooper completed his hat-trick in the 69th minute with another clinical finish when released by Hayes with the Brighton defence again all at sea.
Hooper was hurt in the process and limped off shortly afterwards to a generous round of applause from the Brighton supporters.
Substitute Jake Robinson gave them something to cheer about with a consolation 15 minutes from time, heading in a cross to the far post from Cox.