Mukherjee, who is the first Indian President to have visited the Himalayan neighbour in 18 years, equated the occasional coldness in relations between the two countries as a "difference of opinion in a family".
"Our destinies are inter-linked and there is recognition on both sides of the need to advance common prosperity. India is determined to support Nepal in its pursuit of peace, stability and development.
"Both sides agree that focus should now shift to implementation of ongoing bilateral development and connectivity projects as well as projects for post-earthquake reconstruction of Nepal," he said after completion of visit in Pokhra.
Mukherjee was accompanied by Minister of State for Defence Subhash Bhamre besides Congress Rajya Sabha MP Bhubaneswar Kalita and BJP MPs L Ganesan, Jagdambika Pal and R K Singh.
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The President visited Nepal's capital Kathmandu where he was accorded an elaborate welcome by President Bidya Devi Bhandari herself at the Tribhuvan International Airport with the Vice-President and the Prime Minister.
He also visited Janakpur, which has been the hotbed of Madhesi protests, to offer prayers at historical Janaki temple and Pokhra to meet ex-servicemen of Gurkha regiment.
Mukherjee said he reiterated his invitation to Bhandari to visit India which she accepted with happiness.
"In all my meetings, I found tremendous goodwill and strong desire to advance our excellent bilateral ties for the benefit of our two people," he said.
India remains committed to enhancing its partnership in all areas of priority for the people and Government of Nepal, he said.
"As two sovereign nations, we wish to take forward our relationship on the basis of trust, goodwill and mutual benefit," Mukherjee said.
Mukherjee, who also visited Pokhra where large number of ex-servicemen of Gurkha regiments live, said people of Nepal have contributed immensely to the safety and security of India through their service in the Indian Army.