Shareholders voted for him to replace Dang Tat Thang, who was appointed in March after his predecessor Trinh Van Quyet was arrested for allegedly manipulating the stock market.
Thang now serves as vice president of the company.
Nguyen, brother-in-law of Quyet, has more than 17 years of experience in doing business and used to hold leading positions in many businesses.
He was also a member of the board of directors of FLC Group from 2013 to October 2017 and from June 2018 to June 2020.
FLC said it would focus on restructuring its management model and business plans this year.
Several of its key leaders have been detained amid an investigation into possible stock market fraud that caused "serious damage to investors and affected the operations of Vietnam's stock exchange," according to the Ministry of Public Security.
The company suffered losses of VND465 billion ($19.85 million) in the first quarter, its biggest in the last two years.