Leeds won just of the 16 games that 40-year-old Heckingbottom was in charge for and slipped further out of playoff contention having been well placed in the top six at Christmas.
Leeds had briefly been top of the table in September and remained in playoff contention until January. Manager Thomas Christiansen was sacked in February, but Heckingbottom was unable to reverse the arrest the poor results and reverse the slide down the table.
Fans had finally been hoping to see promotion back to the Premier League, 14 years after relegation.
Managing Director Angus Kinnear said on the matter: "On behalf of the Board of Directors at Leeds United I would like to thank Paul for the commitment and passion he has demonstrated since he joined the club earlier this year.
"Paul came to us during a difficult period in the season and has conducted himself in an exemplary manner despite results not going as any of us had hoped.
"Our objective is to bring in a Head Coach with more experience who can help us reach the goals we have talked about since we became custodians of the club last summer. We are confident of making a quick appointment and we thank our fans for their continued support."