Pools have secured just seven wins from their last 39 matches and Cooper admitted his job was in jeopardy after Tuesday night's 2-1 defeat at the hands of fellow strugglers Bury.
After pondering his situation overnight, Cooper decided that it was in the best interests of the club that he stood down.
A statement on the club's official website read: "It is with reluctance that Hartlepool United today accepted the resignation of first-team coach Neale Cooper.
"Neale stated that he had been very disappointed with the results achieved since the start of the season and, although in several games luck had been against the team, he nevertheless believes they can move on and secure League One status with someone else leading the campaign.
"The club wishes to thank Neale for his commitment and dedication, and wishes him every success in his return to Scotland."
Micky Barron has agreed to take temporary charge of the team, who are bottom of the table after a winless run now stretching to 11 games.
- Sports & Recreation
- Neale Cooper