In 1991, Chakrapong left Funcinpec to join the Cambodian People's Party (CPP) and served as the Deputy Prime Minister of Cambodia between 1992 and 1993.
When the CPP lost the 1993 general elections, Chakrapong led a secession attempt in 1993.
In 1994, he was accused of joining a failed coup attempt (which he denied) which led him to be sent into exile.
After Chakrapong was pardoned in 1998, he founded a private airline company, Royal Phnom Penh Airways.
The airlines later stopped all operations in early 2006.
In 2002, Chakrapong established a royalist party, the Khmer Soul Party.
When the Khmer Soul Party failed to win a single parliamentary seat in the 2003 general elections, Charkapong rejoined Funcinpec and briefly served as Senator in 2005.
In 2006, Chakrapong was expelled from Funcinpec and joined the Norodom Ranariddh Party.
When the Cambodian government pursued legal investigations on the debts Chakrapong accumulated from his airlines, Chakrapong quit politics in 2007.
Chakrapong, who was already a privy councillor to the Supreme Privy Council, then dedicated himself to humanitarian work and supporting royal activities.
In 2013, Chakrapong was appointed member of the Constitutional Council of Cambodia by the King.