The former child star said she felt "honoured" to follow in the footsteps of Pete Townshend and Billy Bragg.
The lecture on 14 October, named after broadcaster John Peel, will air later that night on the digital station.
Church will also be interviewed by DJ Lauren Laverne for a special edition of Weekend Woman's Hour on BBC Radio 4.
"Music is a big part of part of my life," said Church.
"I've had some interesting times during the past 15 years, facing the same problems that many other women face when trying to forge their way in the music and entertainment worlds.
"I'm looking forward to encouraging a healthy debate around this important topic."
This is the third year that the BBC Radio 6 Music Peel Lecture has invited a notable figure to discuss a music-related issue.
The inaugural Peel Lecture was given in 2011 by The Who's Pete Townshend, exploring the implications of digital music media.
Last year Billy Bragg outlined why music and radio need mavericks to keep moving forward.
"Radio 6 Music can challenge the norm, so for Charlotte to question and debate the roles held by women within the music economy encapsulates the opinionated spirit of 6 Music," said James Stirling, 6 Music's head of programmes.
Church will also feature in a preview programme on BBC Radio 4 on 12 October, when Weekend Woman's Hour will be dedicated to exploring the role of women in music.
The show, presented by 6 Music DJ Lauren Laverne, will feature live performances and hear from leading female artists, industry figures and music journalists.
Church's first-hand experience of the record industry began when she found international fame as a child classical singer.
She later rebranded herself as a commercial pop star whose Top 10 hits included Crazy Chick and Call My Name.
Charlotte Church
As well as a singing career, Church also fronted her own Channel 4 chat show
6 Music said Church, now an independent singer-songwriter, was "eminently well-placed to offer informed perspective and insight into what happens, and what is happening, to women in the music business spotlight".
The lecture is part of the Radio Festival, which takes place between 14 and 16 October at The Lowry, Salford Quays.
Hosted by broadcasters Jane Garvey, Fi Glover and XFM's Jon Holmes, it will feature talks from Radio 2's Jeremy Vine, Liam Fisher of talkSPORT, Front Row's Mark Lawson and Magic 105.4's breakfast show host Neil Fox.
"Charlotte has successfully made the transition from a classical artist at a very young age to a successful pop singer in a male dominated world," said Chris Burns, chair of the Radio Festival.
"I'm sure her personal views of the industry today will be thought-provoking."
The Peel Lecture will be introduced by 6 Music presenter Mary-Anne Hobbs and will be available as a free download from 12.01am on 15 October 2013.
John Peel started his broadcasting career at pirate station Radio London before joining BBC Radio 1 for its 1967 launch.
He was famous for championing new talent on his late-night music programme, including Pink Floyd and White Stripes.
