Ms Yingluck was in Phnom Penh to attend the royal cremation of Cambodia's former king Norodom Sihanouk.
The Thai premier met Mr Hun Sen and held bilateral talks at the Cambodian Prime Minister's Office.
The two leaders hailed the good and strong relations between the two countries which has led to the progress of their bilateral cooperation in various fields, which would eventually benefit both mutually.
The Thai leader also said Thailand wanted to cooperate with Cambodia to develop the border areas for prosperity and peace.
Ms Yingluck took the opportunity to thank the Cambodian government in granting a royal pardon and prison term reduction for two Thai activists, saying that the move was considered a goodwill gesture from Cambodia.
Veera Somkwamkid, coordinator of Thailand's Patriots Network, and his secretary Ratree Pipattanapaiboon were arrested on Dec 29, 2010 by Cambodian authorities while inspecting a disputed area claimed by both countries. Both were accused of spying on Cambodia military facilities in Banteay Meanchey province.
Mr Veera received an eight year prison sentence, while his secretary was handed six years jail for espionage and illegal entry.
In accordance with the royal pardon, Ms Ratree was released last Friday (Feb 1) while Mr Veera's prison term is to be reduced by six months, leaving him to remain in jail for another five years.
Ms Yingluck also thanked Phnom Penh for taking good care of 51 Thai prisoners in Cambodia.
The Thai premier later had an audience with King Norodom Sihamoni of Cambodia and Queen Mother Monique Norodom Monineath to affirm the strong relations and cooperation between the two countries.
Ms Yingluck also extended the gratitude to the King of Cambodia who granted pardon and prison term reductions to the two Thai activists.