They met in Addis Ababa, Ethiopia, ahead of the 30th Ordinary Session of the African Union (AU) Assembly.
They reviewed progress in efforts to bring sustainable peace to South Sudan and Somalia.
Mr Guterres acknowledged the South Sudan peace initiatives spearheaded by the Inter-Governmental Authority on Development (Igad) and encouraged member states, including Kenya, not to give up on the peace process.
Mr Guterres asked President Kenyatta to return to the forefront of the continent’s efforts to secure a lasting solution in South Sudan.
The UN Secretary-General also urged all the parties involved in the conflict to work together to find a lasting solution.
President Kenyatta said Kenya was committed to the South Sudan peace process and assured Mr Guterres that the African Union Summit provides an opportunity for Igad leaders to meet and discuss ways of rejuvenating the peace process.
“In essence, it is about Kenya working with the region and partners like the United Nations to secure peace in South Sudan. It is a subject that concerns us as much as it does the United Nations,” he said.
In regard to Somalia, President Kenyatta pressed the Secretary-General for continued support for the African Union Mission in Somalia (Amisom) – which the region sees as the main stabilising factor in the Horn of African nation.
“Stability in Somalia is key for the region and everything we can do to ensure the progress so far achieved is sustained, we should do,” the President said.