Papiss Cisse scored the only goal of the game with a penalty in the sixth minute.
McClaren opted to change his entire XI at half-time to see as many of his players in action as possible in his first game in charge.
The visitors got off to the perfect start when Massadio Haidara was brought down in the box by Gateshead defender Simon Ramsden.
Cisse made no mistake from the spot and Moussa Sissoko should have doubled the Magpies’ advantage but blazed over with the goal gaping having rounded the keeper.
Emmanuele Riviere and Adam Armstrong came close for Newcastle in the second half but it finished 1-0.
Newcastle head out to North America on Saturday for the next part of their pre-season.