It was not immediately clear as to what transpired during the half-an-hour meeting.
Prime Minister Manmohan Singh and Congress President Sonia Gandhi had recently met the President.
Sources said Union Home Minister Sushilkumar Shinde also met Mukherjee and briefed him about security-related issues in the country.
Shinde had recently undertaken a three-day tour of Jammu and Kashmir during which he had met top state government and security functionaries.