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A third minute goal from Ricardo Fuller was enough for Preston to take all three points at Priestfield.
The Jamaican striker pounced on a loose ball and rounded a hesitant Jason Brown before sliding the ball into an empty net.
Preston rarely threatened after their early strike but Gillingham couldn't turn possesion and territory into an equalising goal.
The Gills had numerous shots but struggled to keep them on target and North End keeper Jonathan Gould never had to make a save.
Gillingham's best chance of salvavging a point came in the 55th minute, but the referee waved play on after Mamady Sidibe appeared to be hauled down in the box.
Andy Hessenthaler's men have now lost six home league games this season and are close to being sucked into the relegation battle.