He was the first to offer prayers in the temple this year. He also gifted a miniature replica of the temple to the authorities.
Modi offered prayers at the Shiva temple and performed 'rudrabhishek' which involves bathing the Shiva Linga with Ganges water, milk and honey, among others. Massive destruction had taken place at the Kedarnath Valley in a flash flood in 2013 but the temple premises wasn't much affected.
He was then presented with a miniature replica of the shrine.
Modi was earlier greeted at the airport by Uttarakhand governor KK Paul and chief minister Trivendra Singh Rawat.
During his one-day visit, Prime Minister will also inaugurate a research centre at Ramdev's Patanjali Yogpeeth in Haridwar at 12 PM.
"Tomorrow I will be visiting Dev Bhoomi Uttarakhand. I will begin my Uttarakhand visit by praying at the Kedarnath Temple," the Prime Minister tweeted on Tuesday.
"I will be inaugurating the Patanjali Research Institute at Patanjali Yogpeeth, Haridwar tomorrow, 12 noon onwards. @yogrishiramdev," he said.
On Tuesday, Uttarakhand Chief Minister Trivendra Singh Rawat visited the shrine to review all preparations for pilgrims.
He asked the officials to tighten loose ends, if any, and warned them of stern action if anything was found lacking, reported PTI.
He also asked them to ensure that whoever visits the shrine goes back with good memories.
Kedarnath is one of the most important pilgrimage and religious sites for the Hindus. Nestled in the Himalayas, the pilgrimage site remains closed during winters. Its gates are thrown open for the visitors in the first week of May on the eve of Akshaya Tritiya till the month of October-November.
The temple is the highest among the 12 Jyotirlingas. Kedarnath was the worst affected area during the 2013 Uttarakhand flash floods.