Official sources said that the President cleared the order and sent it to the Ministry of Home Affairs for further action.
The PDP-BJP government had passed a resolution on Wednesday in the assembly after which the state cabinet under the chairmanship of Chief Minister Mehbooba Mufti cleared a draft order for concurrence of the President.
Jammu and Kashmir is the only state which is yet to implement the GST which was rolled out in rest of the country on July 1.
The presidential order, which was concurred by state Governor N N Vohra, relates to the application of certain provisions of the Constitution of India through an order of the President issued under Article 370 that gives special status to the state.
State's Finance Minister Haseeb Drabu had said on Thursday that after the Presidential Order is received, the government will take it to the Assembly for enacting a SGST (state goods and services tax) bill.
Mr Drabu, during a discussion in the assembly on Wednesday, said that the government was not required to bring the resolution but it did so to "get a sense of the House on the issue", a move termed by opposition National Conference and Congress as a "sham".
This was the first time in the history of the Jammu and Kashmir assembly that a resolution, seeking a presidential order on a constitutional amendment, was discussed and passed.