Hundreds of school children were lined up along the way, holding Indian and Bhutanese flag.
During the visit, Mukherjee will hold meetings with Wangchuck and Prime Minister Tshering Tobgay besides other leaders to take bilateral ties to a new level.
Some agreements in education sector are likely to be signed during the trip.
The President is accompanied by a high-level delegation comprising Minister of State for Railways Manoj Sinha, Members of Parliament Mukhtar Abbas Naqvi, Anil Shirole, Mahendra Nath Pandey (all BJP) and Gaurav Gogoi (Congress), besides officials and representatives of a few educational and academic institutions..
Sources said as India is keen to revive the ancient Nalanda University, an agreement will be signed for seeking cooperation from Bhutan in this regard.

Mukherjee's visit to Bhutan comes nearly five months after Prime Minister Narendra Modi's trip to the country. It was Modi's first foreign visit as Prime Minister.
The meetings of the President with the King of Bhutan and the Bhutanese Prime Minister, who will call on him, will provide an opportunity to discuss all issues of mutual interest and ways of further strengthening close bilateral relations.
India shares a unique and special relationship with Bhutan nurtured by successive Kings of Bhutan and Indian leaders.

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