The Congress leader landed at Keshod Airport in Saurashtra and offered prayers at the temple which is about 420 km from the state capital.
Gandhi had visited the Somnath temple during the recent election campaign and his name was found written on the entry register meant for non-Hindus, kicking up a row. The Congress had called it "fake" and the BJP insisted that the leader declare his religious faith before people.
Non-Hindus are allowed to visit the temple but have to first get themselves registered at the shrine's office.
A purported photocopy of a page of the register for non-Hindus had gone viral on social media with the names of Gandhi and senior Congress leader Ahmed Patel written on it.
Gandhi had later said that he and his family were devotees of Lord Shiva.