The President was here as part of the last leg of his three-day visit to West Bengal, Uttar Pradesh and Odisha.
Special arrangements were made for his visit at the famous temple which gets a large number of devotees daily, officials said.
Authorities restricted general public from visiting the temple for some time to facilitate smooth 'darshan' by the President.
Mukherjee spent about half-an-hour in the temple, which consists of Lord Jagannath, Balabhadra and Subhadra deities.
The President was accompanied by his son and Lok Sabha MP from Jangipur (West Bengal), Abhijit, Minister for Finance and Public Enterprises, Odisha, Pradip Kumar Amat and officials of Rashtrapati Bhavan and the state government.