He was received by senior BJP leader LK Advani and welcomed by the temple community in the backdrop of hymns and drum rolls.
Mukherjee performed puja at the Lord Shiva's temple, which is one amongst 12 'Jyotirlingas' (the radiant sign of Shiva) as per Hindu mythology.
He also paid floral tributes at the statue of Sardar Vallabhbhai Patel in front of the temple.
The President is on his maiden visit to Gujarat and Diu after assuming country's top office on July 25, 2012. Earlier in the day, Mukherjee addressed a function in Sabarmati Ashram in Ahmedabad.