McDowell joined the BPI in September 2009 as public affairs and comms executive, working her way up to head of PR in 2014.
McDowell’s new company will offer strategic comms advice, PR support, media services, business development and project management for companies in the creative industries.
She will continue to act as a PR consultant for the company.
BPI and BRIT Awards chief executive, Geoff Taylor, said: "Lynne's professionalism and dedication were huge assets to the BPI and we are delighted that she will continue to consult for us. We wish her the very best in this new chapter of her career."
McDowell said: "After more than five wonderful years at the BPI, I feel it is time for a new adventure. Setting up my own PR company feels like the next logical step in my career and I’m excited to already be working with some of my favourite music companies, while remaining a consultant for the BPI."