He continued to participate in the development of the economic legislation of the Republic of Azerbaijan. Akhundov took part in the development of antitrust legislation and of laws including "On the Property" and "On the Committee for State Property", which ensured the country's transition from a centrally planned economy to a market economy. After the post-graduate studies at the University of Texas (Austin, Texas, United States), he began his career in the banking system of the Republic of Azerbaijan. In 1993 he headed the International Banking Operations Department at the Industrial Investment Bank of Azerbaijan. In 1994 he took the position of Director of the Department for Regulation of Foreign Exchange Transactions and International Financial Institutions in the National Bank of Azerbaijan (NBA). Later, Akhundov was appointed Director of the Department for Monetary Policy and Regulation of Foreign Exchange Operations in the NBA. From August 1994 to September 1995, Akhundov was the Deputy Chairman of the National Bank of Azerbaijan. While working at the National Bank of Azerbaijan, he led the bank's team at the negotiations of the NBA with the IMF and the World Bank. Being one of the founders of the first monetary program of the NBA, he personally developed and presented the law "Regulations on Foreign Exchange Regulation" to the Parliament of Azerbaijan. Under the leadership of Akhundov, a new national payment system and the first payments balance of the country were introduced. As the Chairman of the Board of the Baku Interbank Currency Exchange, he organized the first auction, which laid the foundation for the inter-bank foreign exchange market. In 1995, Fuad Akhundov headed the International Bank of Azerbaijan (IBA). By 2001, the IBA had become the leading bank in the Republic of Azerbaijan, with a market share estimated at 2/3 of the country's banking capital, and with about 50% of retail deposits. In 1996 the bank launched a credit cards program, Azerbaijan's first ATM was installed the same year, and the first international credit cards were issued in 1997. Later, the IBA served over 2 million cardholders and controlled 90% of the country's market. As a strategy for retail banking operations, the scheme of payment of utility bills was launched in Azerbaijan's capital, the city of Baku, in 2000. The bank was recognized as the best regional bank in the CIS (Commonwealth of Independent States) in the field of management, and as the bank with the best management information system and IT system in the CIS countries. According to "Euromoney" magazine, it was recognized as the "Best Bank in Azerbaijan" in 1998, 1999, 2000, and was nominated "Bank of the Year" in "Banker" magazine.