He joins from quoted property firm Mapeley where he was chief financial officer.
Before the appointment, the finance function was run on an interim basis by Paul Truman, who remains at the firm.
Cooke joins Bestinvest in the wake of a number of changes following its 3i-backed management buyout last August.
Former Zurich chief executive Ray Greenshields joined as chairman in November but the firm has seen a number of departures, including senior members Dominic Cummings, Justin Modray and Mike Neumann.
Chief executive officer Andrew Barnes says: “Stephen brings a great deal of experience to Bestinvest and will be a key appointment for us as we develop the business.
“He will help us in continuing to grow and expand our services to the investing community. He has the expertise that will help the whole team meet the demanding targets we have set for Bestinvest in 2008 and beyond.”