In his message on micro-blogging site Twitter, Mukherjee said he is confident that in coming years, both countries will continue to work together to further strengthen bilateral relations.
"Congratulations and warm felicitations to Mr Maithripala Sirisena on his election as President of Sri Lanka. Best wishes for success of endeavors for peace and development in Sri Lanka and for progress and prosperity of its people," Mukherjee said.
President Mahinda Rajapaksa on Friday conceded defeat in Sri Lanka's presidential race, with cumulative results showing opposition candidate Sirisena ahead.
Sri Lankans had yesterday voted in large numbers in the bitterly contested presidential election in the biggest political shake-up in over a decade.