He was 63.
He is survived by wife and two sons.
Singh took over as Jathedar of Takht Kesgarh Sahib in 2013.
The Jathedar had undergone surgery for brain tumour last year, Shiromani Gurdwara Parbandhak Committee chief Kirpal Singh Badungar said.
He had not been keeping well for sometime and was admitted to hospital again. He breathed his last this afternoon, he said.
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His mortal remains will be cremated take place tomorrow at 11 AM in Anandpur Sahib, Badungar said.
In a condolence message, Amarinder described the Jathedar as a great Sikh scholar and a theologian, who was well versed with Gumat, Gurbani and Sikh tenets.