Grant McCann's side are yet to concede a goal and are one of only two third-tier clubs to earn nine points from their opening three fixtures.
It is the first time since October and November last year that Hull have won three leagues games in a row under McCann.
Hull took the lead at Northampton - who had picked up four points from the first six on offer - when George Honeyman provided the cross for Keane Lewis-Potter to nod home with 34 minutes played.
Honeymonen turned from provider to scorer on the stroke of half time as he latched onto a pass from debutant Hakeeb Adelakun to double the lead.
Substitute James Scott almost added a third as the game ticked past the 70-minute mark but his glancing header was wide of the target.
Scott had another opportunity but his effort from Lewis-Potter's cross was well held by Steven Arnold in the Northampton goal.
Hull sit second in the League One, only kept off the top spot - occupied by Ipswich Town - on goal difference.
Next up for McCann's side is the visit of Plymouth Argyle as they look to extend their perfect start to the league season.
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