Although it was goalless at the break, the Villagers responded to four defeats in-a-row by taking the game to the hosts.
Thompson shot just wide from Taron Hare's cross, and Danny Clarke forced Sam Johnson into a good save.
It was no surprise when Thompson gave North Ferriby the advantage in the 49th minute. The deadline-day signing marked his first goal for the Grange Lane club by rounding the goalkeeper and slotting in from a tight angle.
Gus Mafuta's late strike almost levelled the scores, but North Ferriby held on for the win.
Report supplied by the Press Association.
Match ends, Gateshead 0, North Ferriby United 1.
Second Half ends, Gateshead 0, North Ferriby United 1.
Connor Oliver (North Ferriby United) is shown the yellow card for a bad foul.
Substitution, North Ferriby United. Ryan Fallowfield replaces Connor Robinson.
Mitch Brundle (Gateshead) is shown the yellow card.
Substitution, Gateshead. Adam Wrightson replaces James Bolton.
Substitution, North Ferriby United. Ryan Kendall replaces Reece Thompson.
Substitution, North Ferriby United. Danny Emerton replaces Jake Skelton.
Goal!  Gateshead 0, North Ferriby United 1. Reece Thompson (North Ferriby United).
Substitution, Gateshead. Gus Mafuta replaces Rhys Oates.
Substitution, Gateshead. Danny Johnson replaces Sam Jones.
Second Half begins Gateshead 0, North Ferriby United 0.
First Half ends, Gateshead 0, North Ferriby United 0.
Patrick McLaughlin (Gateshead) is shown the yellow card for a bad foul.
Sam Jones (Gateshead) is shown the yellow card for a bad foul.
First Half begins.
Lineups are announced and players are warming up.
Reece Thompson's second-half goal handed North Ferriby their first ever away win in the fifth tier as they beat struggling Gateshead.