Former Sri Lanka captain Atapattu has been in interim charge of the team since Paul Farbrace's departure to join Peter Moores' England set-up in April.
He has since led the side to one-day international and Test series victories in England and against Pakistan, and recently expressed his confidence in taking the role permanently.
A slight blot on his copybook came in the form of series defeats while touring South Africa.
Sri Lanka Cricket (SLC) confirmed on Tuesday they were to hold interviews with Atapattu and one more unnamed candidate for the role. Reports had suggested former Australia coach Mickey Arthur had been considered for the job.
A subsequent SLC statement read: "Sri Lanka Cricket wishes to announce that as per the recommendations of the special committee appointed to select the national head coach, The Executive Committee of SLC unanimously approved and appointed Mr Marvan Atapattu to the position of national head coach of Sri Lanka Cricket with immediate effect."
Atapattu is Sri Lanka's first native coach since Roy Dias - who led the country into the 1999 Cricket World Cup.