After the military overthrew the government of Thaksin Shinawatra, he remained in Singapore where he was attending the annual meeting of the World Bank/International Monetary Fund.

Thanong became the Dean of the Graduate School of Business Administration or NIDA Business School, National Institute of Development Administration (NIDA).

From April to August 2007, Thanong was a visiting professor at the International Graduate School of Social Sciences, Yokohama National University, Japan.

Thanong was invited by the government of Premier Chavalit Yongchaiyudh to be finance minister from June to October 1997, the height of the Asian financial crisis.

He served as finance minister in the government of Thaksin Shinawatra for a second term from August 2005 until the military coup of September 2006.