Hooper punished Brighton for poor defending with his treble after Martyn Woolford gave the Iron the perfect start with a fourth-minute lead on his first league start.
Substitute Jake Robinson grabbed Brighton's consolation with a far-post header 16 minutes from time as the Seagulls crashed to their first defeat of the season.
Brighton went behind for the first time this season early on as Woolford converted a low cross from Paul Hayes at point blank range.
The Seagulls' problems increased in first half stoppage time when former Southend striker Hooper struck with a fine individual effort after getting the better of defender Colin Hawkins.
Scunthorpe surged into a three goal lead on 54 minutes through Hooper who punished more slack defending to fire past keeper Michel Kuipers from close in and Hooper completed his hat-trick on 68 minutes with a low shot following more hesitation from the edge of the Brighton area.