A bench comprising Justices AK Sikri and Ashok Bhushan rejected the Gorkha Janmukti Morcha's plea saying it was not a fit case for relief.
"It cannot be said to be a case of individual persecution by the state," the bench said while pronouncing the order.
The top court had on November 20 restrained the West Bengal police from taking any coercive steps against Mr Gurung.
The GJM leader had claimed in the top court that he was being politically persecuted by the West Bengal government.
The GJM central committee had recently suspended Mr Gurung for six months and appointed Binay Tamang as the party's new president.
The police had earlier claimed that Mr Gurung and some of his aides were absconding after being booked under the Unlawful Activities (Prevention) Act in connection with the violence in Darjeeling hills during the recent agitation for a separate Gorkhaland.
Mr Gurung has approached the top court seeking an independent probe into the alleged killings of Gorkhaland supporters during the protests.