The surprise visit marks the highest-level contact between the United States and North Korea since 2000.
Mr Trump is expected to hold a summit with Mr Kim by June. Details are being worked out, the US president said.
South Korea has also signalled that it may pursue a formal resolution of the longstanding conflict on the peninsula. President Moon Jae-in and Mr Kim are due to meet next week.
North Korea will hold a plenary meeting of its ruling party's central committee tomorrow.
Such meetings are held to decide important policy issues.
The US president earlier gave his "blessing" for the talks between the South and North to discuss a peace treaty to formally end the 1950-1953 Korean War.
Mr Pompeo's trip took place after he was nominated by Mr Trump to replace Rex Tillerson as secretary of state.
Very little is known about the talks other than that they were to prepare for the forthcoming Trump-Kim summit.
Mr Pompeo is predicted to be confirmed as the top US diplomat by the Republican-controlled Senate in the coming weeks, although Democratic opposition to the conservative's candidacy is strong.
Senator Robert Menendez, the top Democrat on the Foreign Relations Committee, said he did not think Mr Pompeo's "past sentiments" reflected American values.
The hawkish CIA chief is known for his opposition to same-sex marriage and has made controversial remarks about Islam.
News of Mr Pompeo's visit is likely to overshadow delicate talks with Japan, a key US ally and neighbour of North Korea.
There have been fears in Tokyo that Mr Trump's plans for bilateral talks could sideline Japan, and Prime Minister Shinzo Abe is currently in Florida for talks with the US leader.
Relations between the two men appeared cordial on this, the second time that Mr Trump has welcomed Mr Abe to his Mar-a-Lago resort in Florida.
Mr Trump insisted on Tuesday that the two countries were "very unified on the subject of North Korea", and Mr Abe praised the US president's handling of the North Korea issue.
However, observers say Mr Abe's goal for his US trip will be to persuade the US president as much as he can not to sway from the West's hard line on Pyongyang.