The president reached the temple, about 55 km from state capital Bhubaneswar, at 7.10 a.m.
He was greeted by officials and temple functionaries.
Mukherjee offered prayers to different deities inside the temple complex. He visited the sanctum sanctorum and offered prayers to Lord Jagannath, his brother Balabhadra and sister Subhadra.
"He also lit diyas (lamps) at the temple," Laxmidhar Pujapanda, public relations officer of the temple administration, told IANS.
The president spent about 30 minutes inside the shrine.
Other devotees were barred from entering the temple premises during the president's visit.
Mukherjee who arrived in Odisha Friday on a two-day visit spent the night at the Raj Bhavan in Puri.
On Friday evening, he visited the beach and saw a sand sculpture created by internationally acclaimed sand artist Sudarsan Pattnaik.
The president is scheduled to attend the second convocation of the Indian Institute of Technology-Bhubaneswar Saturday.
He is also scheduled to attend the convocation of Bharatiya Vidya Bhavan's Centre for Communication and Management before returning to New Delhi later in the day.
This is Mukherjee's second visit to Odisha after becoming president. He had earlier visited the state in April.
--IANS (Posted on 07-09-2013)