The watercolours by the architect and artist, as well as book works, come from voluminous Glasgow School of Art (GSA) Archives and will be the inspiration for a new show that will run from June to September.
The watercolours and editions of an artist-produced publication called The Magazine, which were created by Mackintosh and his contemporaries in the late 1890s, will be shown as part of a show called Cabbages in an Orchard: the formers and forms of Charles Rennie Mackintosh along with work by the contemporary artist Graham Fagen.
The show is part of the nationwide contemporary art show Generation, which is being run by the National Galleries of Scotland and partner galleries next year.
Scottish artist Fagen, who was part of the Scottish show at the Venice Biennale in 2003, among many other exhibitions, will create a new series of artwork himself after studying the work of Mackintosh and his contemporaries.
Mackintosh, born in 1868, trained as an architect at a local business but studied art and design at evening classes at the Glasgow School of Art.
At art school Mackintosh and his friend and colleague Herbert MacNair also met the artist sisters Margaret and Frances Macdonald.
Mackintosh's work, including plant drawings, were published together in a periodical called The Magazine, and these images will be a key part of the new exhibition.
It will feature works including the Tree of Influence, and Cabbages in An Orchard.
Jenny Brownrigg, exhibitions director at the GSA, said: "In the 2011 essay How I Fell Out and In With CRM, Graham outlined his rocky relationship with Charles Rennie Mackintosh as a student at The Glasgow School of Art, and his subsequent re-alignment with Mackintosh's way of working.
"The short period Graham spent in GSA's Special Collections and Archives researching for the essay in 2011 led to a rapprochement between himself and Mackintosh.
"One shared area Graham identified was their common use of image with text as a tactic.
"We were delighted to be able to offer Graham the opportunity to come back and continue his research, and to create a new body of work for Generation to be shown alongside Mackintosh's original watercolours and book works."
Fagen said: "I feel privileged to be offered the opportunity to research Mackintosh and his contemporaries in the GSA archive.
"I'm filled with an equal measure of excitement and trepidation at the chance to exhibit new work responding to this experience."
The Magazine was produced by a loose group of students, friends and relations who met at the Glasgow School of Art in the late 1880s and early '90s.
They were mostly women, with almost all of them living in the West End of Glasgow.
Lucy Raeburn was the The Magazine's editor and her sister Agnes was on the school's register from 1887 to 1902. Agnes was one of a group of female students who attended GSA director , Francis Newbery women's figure class in 1890-91.
Cabbages in an Orchard: the formers and forms of Charles Rennie Mackintosh and Graham Fagen will be staged at the Mackintosh Museum from June 28 to September 27 next year.