The Cobblers took the lead after six minutes when Gavin Johnson saw his shot deflected to Scott McGleish and he squared the ball back for Ryan Gilligan to shoot home from eight yards.
Play was quite boring for the next 15 minutes with both sides finding it hard to get to grips with the game.
However on 20 minutes Eoin Jess was inches wide with a low shot from 20 yards out and a minute later Rushden went close when Daniel Grainger's cross was headed on by Drewe Broughton but Magnus Okounghae was unable to convert.
On 28 minutes veteran Ian Taylor was just wide with a shot from just outside the box while two minutes later Broughton saw his header deflected from a corner and from the resultant kick his bullet header was brilliantly tipped over by Lee Harper.
On 33 minutes Taylor put McGleish through but Jamie Young made an excellent save.
Rushden tried hard to get back into the game and former Cobbler Dave Savage tested Harper with a fierce shot from 20 yards.
On 52 minutes tricky work by Rushden winger Marcus Kelly ended with the winger shooting inches past the post.
Rushden equalised against the run of play on 62 minutes when Chris O'Grady put Savage through and the midfield man raced on to shoot past Harper.
Northampton went in front for the second time in the 79th minute when David Hunt saw his cross headed into his own net by Rushden defender Rob Gier.
The goal seemed to knock the stuffing out of Rushden and Northampton put the game beyond doubt when Hunt's free kick found Taylor whose header was not held by Young and McGleish followed up to score from virtually on the line.
Rushden were unable to come back from this double blow and Northampton held on for a good victory.