Mukherjee was received at the airport by state minister for planning Rachpal Singh and Chief Secretary Sanjay Mitra.
The President left the city for Murshidabad district by a helicopter to attend a series of functions.
His engagements include inauguration of a new building of Domkal Girls' College and address to students of Krishnath College at Berhampore.
Mukherjee will felicitate a group of industry leaders at the formal inauguration of the Indian Institute of Engineering Science and Technology (IIEST) at Shibpur in Howrah district tomorrow.