The ex-Velvet Underground frontman is celebrated by the station from October 14-21 and Reed co-hosts the New York Shuffle series with producer Hal Willner, who worked on his Berlin concert film.
"Playing new and older music with the knowledgeable compendium of Hal Willner is a great pleasure," Reed said.
"This is music for the sake of beauty, power and splendour. Object - tune in, tune up and heighten the emotional and physical world through the music we all know, and experience the healing.
"From hip-hop through to Albert Ayler through to Clara Rockmore. Welcome to our world BBC Radio 6 Music."
Head of programmes at BBC Radio 6 Music James Stirling added: "Lou Reed's contribution to music is huge.
"His ability to unite the worlds of music and art, coupled with his song-writing ability, has inspired many of the artists so vital to 6 Music's listeners.
"I am delighted that we can bring his radio show to our audience."
In addition to the New York Shuffle series, 6 Music will host a number of other related programmes during the week, including:
- The First Time with John Cale. Founder member of The Velvet Underground John Cale OBE talks to Mike Everitt about his experiences during his 30-year career.
- Lauren Laverne plays her favourite Lou Reed and Velvet Underground cover versions.
- Shaun Keaveny unveils 6 Music's version of Lou Reed's 'Perfect Day', starring all of 6 Music's presenters.
- Marc Riley, Jarvis and Huey Morgan host themed shows exploring the influences and themes of Lou Reed's music, New York, art and the musicians he worked with.