The Essex club have announced the former Luton Town number two will take up another role elsewhere.
He leaves the club having just guided them to their biggest win of the season.
Assistant manager Danny Searle has agreed to take over as the Iron look to win their fight against relegation.
Chairman Lee Harding said: "When Hakan offered to help in October, we'd won only once in fifteen matches and then, with the same players, immediately picked up seven points from the next three games.
“Sadly, with some players not secured on contract, it was then easy for other clubs to tempt some away, and results then suffered.
“Recently we've seen the benefits of the re-building work that both Hakan and Danny have been putting in place and results over the past month or so have started to improve. We wish Hakan all the best for the future.”
Speaking after the 4-0 victory over Barnet, there were no signs he was about to call it a day at Cressing Road.
“We still believe,” said the manager, who returned to the club when Brad Quinton was let go back in October.
“We now need consistency and we need to keep the wins coming if we can.
“If we do that I think we can still pull away from the relegation-zone, it’s not too late and we have given ourselves something to work with
“The performance was excellent but now we need to build on this and see where it takes us.”
Next up for Braintree is a trip to Hartlepool before title chasers Salford City visit Essex.