Richard Evans had been with the company for a decade. He was promoted to head up its worldwide electronic trading arm in July.
Based in London, the 34-year-old had a growing reputation in the City having been a co-founder of the alternative trading platform Turquoise and he is one of the most high-profile casualties of Citigroup's recent downturn.
His departure comes around two weeks after the company announced it would be cutting 52,000 jobs worldwide in a bid to cut costs and boost profitability during the current downturn.
Those layoffs were on top of 23,000 job losses already implemented between January and September, Reuters reported.
Nevertheless, Citigroup has said Mr Evans' departure does not mean it will be abandoning electronic trading. In a statement, the company said it remains "strongly committed to the electronic execution business".