"I recognise your sincere desire to strengthen our good neighbourly relations and overcome any incidents in relations between our two countries," Grabar-Kitarovic said in her message, according to a press release from her office.
The message was conveyed by the Croatian president's foreign policy adviser, Dario Mihelin, to his Serbian counterpart, Ivan Mrkic.
The Croatian flag was burnt outside a courthouse in Belgrade on Wednesday by the Serbian Radical Party leader and war crimes indictee, Vojislav Seselj.
"As the heads of state, we have particular responsibility for the overall atmosphere in relations between our countries and I hope that through our joint efforts we will further encourage our respective governments to finally close some of the chapters from the recent past, which I firmly believe should be addressed by neighbours who are turning towards a common European future. In that regard, I would like our future meeting to be a true step forward in our relations, which I am certain is what we both strive for," the Croatian president said.