Suu Kyi, the Myanmar Foreign Minister, also met Prime Minister Narendra Modi at Rashtrapati Bhavan where she was accorded a ceremonial reception earlier.
"India and Myanmar are close neighbours and have a good long standing relationship with each other," Mukherjee said in his meeting with Suu Kyi.
Congratulating her on the landmark victory in the General Elections held in November, 2015, Mukherjee said India "appreciates the spirit with which the people of Myanmar have responded in the elections and that he was happy that the process of democratization was being strengthened in Myanmar".
He said Myanmar's transition to full democracy would take time to achieve and "India stands by Myanmar in this process."
Seeking India's support, Suu Kyi said, "Myanmar seeks the cooperation and support of India as its people look forward to progress and change for the betterment of their lives."
Suu Kyi, who is on a three-day visit here post the Brics-Bimstec Summit in Goa, also met External Affairs Minister Sushma Swaraj and Women and Child Development Minister Maneka Gandhi.
She also visited the Raj Ghat to pay tribute to Mahatma Gandhi.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)