Enhancing projects between South Africa and Botswana is important for economic development, President Jacob Zuma said.
"We need to prioritise cross-border projects to ease movement of goods and services," Zuma said at a bi-national commission with his Botswana counterpart President Ian Khama in Pretoria.
The three-day meeting saw the two countries discussing cooperation in sectors such as energy, trade and investment, education, defence, water and the environment, and immigration, Zuma said.
Zuma said there was a need to strengthen co-operation within organisations in the region and across the continent.
Khama said he would ensure the two countries co-operated at the highest level.
"I will do everything in my power whilst I am still in office to enhance these relations."