Tight security cover has been thrown around the capital for Mukherjee's visit, the first to Jammu and Kashmir after he took over as President on July 25 this year.
The President was received at the airport by Governor N N Vohra, Chief Minister Omar Abdullah and his ministerial colleagues.
Mukherjee will attend tomorrow the convocation of Kashmir University which is taking place after a gap of over three years.
The previous convocation was held in June 2009 with Vice-President Hamid Ansari in attendance.
During the convocation, a total of 214 gold and silver medals will be awarded to students for topping their respective disciplines in the past three years.
In addition, 234 PhDs, 399 M Phils, 21240 post graduates, 119799 gradutes and 93 diplomas will also be honoured.
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Ahead of the President's visit, an elated Vice Chancellor of the University, Prof Talat Ahmed, said it is an extreme honour to have the Head of State among students and faculty members.
"It will be an extremely important visit and will give a boost to academicians and faculty members besides exposure to students," he told PTI.
Ahmed said his attempt is to bring the Kashmir University under national spotlight.
Governor N N Vohra is hosting a banquet for the President tomorrow.
Mukherjee will also review the Dal Lake conservation project and interact with intellectuals and political leaders before returning to Delhi on Friday.