Mr Troughton joined Alliance Trust Investments in February 2008 and sought to build an open-ended funds arm around its previously anonymous investment team.
But last year, ATI closed its UK Equity Income, Asia-Pacific and Japan funds. Its offering is now focused on global equities, fixed income and socially responsible investing. It manages £1.6 billion for external investors.
Alliance said Mr Troughton is leaving for another post in the industry. Trust chief executive Katherine Garrett-Cox will oversee the business until a replacement is found.
She said: "We remain committed to the long-term growth of the ATI business."