Atapattu's resignation comes after the island nation lost back-to-back Test series against continental neighbours Pakistan and India in the last three months.
Atapattu's resignation has been accepted by Sri Lanka Cricket's interim chief Sidath Wettimuny.
"We would like to inform you of the resignation of Mr. Marvan Atapattu from the post of Head Coach of the Sri Lanka Cricket Team which has been accepted by Sri Lanka Cricket," the SLC said in a statement.
He had also worked as a batting coach of the team from 2011 and was also the interim head coach for some time before he was assigned full charge.
"Mr. Atapattu was appointed to this position in October 2014, previously serving as the Batting Coach to the team from 2011 and as Interim Head Coach for a brief period from April 2014 after Mr.Paul Farbrace resigned," the SLC said.
SLC thanked Attapattu for his service to the national team.
"Sri Lanka Cricket thanks Mr. Atapattu for his efforts as Head Coach and Batting Coach of the Sri Lanka Cricket Team, and we wish him every success in all his future endeavors," the Board said.
According to reports, SLC is likely to approach former Sri Lanka batsman Chandika Hathurusinghe for the post of chief coach as he has done remarkably well with the Bangladesh national side.
The other name that is doing rounds is of Graham Ford.
The 44-year-old Atapattu has played 90 Test matches and 268 ODIs for Sri Lanka scoring 5502 and 8529 runs respectively.
