The cover of the vinyl, appearing with the 12 September issue, features an exclusive design originally drawn by Doherty in his own blood, while the B-side has an interview with the band discussing its new album.
The deal follows an earlier tie-in with the White Stripes, who released 120,000 copies of their single Rag and Bone as a limited-edition vinyl with the 6 June edition.
NME editor Conor McNicholas said the edition was bound to become an "instant collector's item".
"Yet again NME is leading the music and publishing industries by creating big release events to excite music fans," he said.
"Pete is very close to our hearts and we're made up to be working with Babyshambles and Parlophone in releasing this unique track."
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