The event will be held on Fridays under the famous glass canopy at the station 22 million people pass through every year.
Stalls will sell handmade crafts, locally sourced cold and hot food, and there is to be a rotating programme of attractions including an art fair and vintage clothing sales.
It will be open from 11am to 7pm and be held in a large space at the rear of the station, behind the ticket office, close to platform 2.
Vicky MacDonald, of LocalMotive Markets, which will run the event, said: "We want the market to showcase the amazing products and services local businesses with a conscience have to offer. More than 22 million people use Waverley train station every year and we want to give them an alternative shopping experience that brings all the variety, passion and creativity of the local entrepreneurial spirit under one roof."
Edinburgh Waverley last hosted a market in 1974. It was situated on the side of the station closest to Princes Street but closed to make way for Princes Mall.
Juliet Donnachie, Waverley station manager for Network Rail, said: "We're thrilled to be able to announce this innovative new venture in partnership with LocalMotive Markets. Recent improvements within the station have left us with us with a fantastic vacant space which we're pleased to be able to use for this purpose."
LocalMotive Markets say there are still some stalls available for traders offering quality food or arts and crafts, and there was even a space for a massage therapist. Prices for traders ranged from £30 to £60 depending on the size of the staff. The first market will be on May 2.