Pools failed to clear and when Joey Gudjonsson fed the ball back into the area, Pilkington got behind the defence to shoot low past Scott Flinders on 11 minutes.
The mid-table home side failed to spark in the opening half, but pressed the Terriers back throughout the second period.
Gary Liddle sliced a good chance wide and then Andy Monkhouse broke away clear but his low shot narrowly failed to find the target.
Top scorer Antony Sweeney then found himself in front of goal, but the dominant Peter Clarke blocked his effort as Huddersfield held on.
Hartlepool 0-1 Huddersfield: Match Report - view commentary, squad, and statictics of the game as it happened.