Mukherjee handed over his nomination papers to Vivek Kumar Agnihotri, Rajya Sabha Secretary General and Returning Officer for the Presidential elections.
Soon after completing the process, Mukherjee thanked parties like SP, BSP, JD(U), CPI-M and Shiv Sena for reposing faith in him.
"I am grateful to them as they have reposed faith in me to occupy the office which was occupied in the past by great stalwarts of this country.
"I only wish at this time that let me have the blessings of God and cooperation of all at this juncture," he told reporters at the Parliament House.
Four sets of nomination papers, signed by as many as 480 MPs and MLAs, including Union Ministers, Chief Ministers, Congress Legislature Party leaders and PCC chiefs were submitted by Mukherjee.
Convenor of the opposition NDA and JD(U) President Sharad Yadav was the first signatory on one set of nomination papers followed by Defence Minister A K Antony.
Samajwadi Party chief Mulayam Singh Yadav and BSP supremo Mayawati have also signed the nomination papers.
As a matter of abundant precaution, each set of nomination papers has 60 proposers and 60 seconders against 50 proposers and 50 seconders as required under election rules.
SP supremo Mulayam Singh Yadav, RJD chief Lalu Prasad, RLD chief Ram Vilas Paswan, Congress general secretary Rahul Gandhi and union ministers such as P Chidambaram, Farooq Abdullah, Ajit Singh, E Ahamed, A K Antony, Pawan Kumar Bansal, Ashwini Kumar were present at the time of Mukherjee filing his nomination papers.
As expected, UPA ally Trinamool Congress, which has decided not to back Mukherjee, was not present.
SP leader Ram Gopal Yadav, BSP leader Satish Chandra Mishra, NCP leader D P Tripathi were among others who witnessed the filing of nomination papers.
Parliamentary Affairs Minister Pawan Kumar Bansal has been appointed as Mukherjee's authorised representative.
Pics: Prabhas, Tamannaah Bhatia at 'Baahubali 2' first look launch at MAMI
'Ae Dil Hai Mushkil' photos: Aishwarya, Anushka, Karan get candid at MAMI
Photos: Huma Qureshi, Neha Dhupia and other celebs at MAMI
Photos: Amy Jackson, Daisy Shah at Mumbai airport
Photos: Sridevi, Irrfan and other celebs at 'Mughal-e-Azam' screening