In his condolence message on the passing away of Koirala, Mukherjee said he led Nepal during the crucial period of political transition.
"Under his stewardship of the Government of Nepal, considerable progress was achieved in the fields of hydropower and connectivity," the President said.
In his passing away, Nepal has lost a leader who dedicated his life to Nepal's progress and development, Mukherjee said.
"He led Nepal during the crucial period of political transition and Constitution promulgation. The simplicity of his life holds a lesson for all of us," Mukherjee said.
"The people of India share the sorrow and grief of the people of Nepal over the loss of Sushil Koirala. Please accept my heartfelt condolences," the President said.