Kamarai Swyer dragged wide from an early Kyle Edwards cross but the first half took a while to warm up on a bitterly cold afternoon at Sixfields.
Northampton edged a scrappy game and carried a threat through Edwards, who saw one shot blocked and another well saved, but clear-cut chances were few and far between.
Stockport boss Dave Challinor, clearly unhappy with his side’s performance, made four substitutions at the break but County remained without a single shot after an hour.
The away side’s first effort finally arrived after 65 minutes and it nearly yielded the breakthrough when Malik Mothersille’s well-struck attempt forced home goalkeeper Ross Fitzsimons to tip over.
Ben Osborn missed the target from the edge of the box while Ben Hinchliffe saved with his legs from Joe Wormleighton at the other end as the points were shared.