Under-fire Hopkins saw his misfiring team ripped apart at the Priestfield Stadium by a side who had previously not won at home since August.
The Bantams remain rooted of the bottom of League One after picking up just 10 points in 16 matches this term.
Hopkin decided to keep his counsel rather than give the City supporters a reaction to this embarrassing defeat.
It was a fifth successive league defeat for the Bantams and sixth in a row in all competitions.
Hopkin had been handed a vote of confidence by joint-owner Stefan Rupp but the Bantams have lost eight league games out of 10 since the 48-year-old took over the managerial reins from Michael Collins in September.
Regan Charles-Cook curled the ball home three minutes into the second half after the visitors had wasted chances to lead before the break.
Then Tom Eaves bagged a brace, having had a 62nd-minute penalty saved by Richard O’Donnell.
Substitute Elliott List was also on the scoresheet in the rout as the home team claimed their biggest win since September, 2015.
Gills chief Steve Lovell praised his side for their comprehensive victory, having gone three games without a win in the league.
“I expected it, we will only get better,” said Lovell. “It will take a bit of time, but we’ll get there. It’s been a difficult week for us, but this was a great result.”
Gillingham: Holy, O’Neill, Ehmer, Zakuani, Fuller, Bingham (Parrett 83), Oldaker, Byrne, Charles-Cook (Nasseri 74), Eaves, Hanlan (List 66). Unused substitutes: Lacey, Mbo, Hadler, Ogilvie.
Bradford City: O’Donnell, Wood, O’Connor, Knight-Percival, Isherwood (Brunker 73), Wright, Akpan, O’Brien, Ball (Gibson 85), Doyle (Seedorf 80), Payne. Unused substitutes: Sykes-Kenworthy, Staunton, Goldthorp, Maltby.
Referee: L Collins (Surrey).