Flynn has been at the firm for nine years and was head of retirement services.
Sales director and board member Colin Cameron has also left the firm, along with corporate seminar presenter Tina Gilchrist.
Origin has been hit by a rash of departures in the past 12 months, including finance director Jim McGuinness, who stepped down from his role at the Aegon-owned firm last November.
The firm also announced the loss of four senior managers and around 14 advisers in May.
Managing director Stephen Greenstreet says the firm has made up for the departures with 27 new additions in 2008.
He says the group has also established regional sales roles to help improve service and advice to clients.
New additions include Warren Page, who joins as sales director from Barclays Financial Planning.
Greenstreet says: “As part of the ongoing enhancements to our client and TCF proposition and our improved business efficiencies, Nick Flynn, Colin Cameron and Tina Gilchrist are to leave Origen.
“Each one is leaving for different reasons to pursue other interests and we wish them well.”