The two leaders also reviewed the latest regional and international developments.
The Singaporean Prime Minister is due to attend a summit between the Gulf Cooperation Council and the Association of Southeast Asian Nations on Friday in the Saudi capital.
“At the Asean-GCC Summit, the Asean and GCC Leaders will discuss ways to strengthen relations and expand co-operation to new and emerging areas such as the green and digital economies,” Singapore's foreign ministry said.
Mr Lee will also be briefed on Saudi Arabia’s Vision 2030 strategy for diversifying its economy, the ministry added.
His visit to Saudi Arabia follows another high-level meeting between the Crown Prince and Vietnam's Prime Minister, Pham Minh Chinh, who arrived to Riyadh on Wednesday.
Mr Lee will visit the UAE next, after an invitation from President Sheikh Mohamed.
Earlier on Wednesday an urgent ministerial meeting of the Executive Committee of the Organization of Islamic Cooperation was held in Jeddah to discuss the military escalation in Gaza and the mounting attacks on civilians, including an air strike on a hospital that killed more than 500 people.
On Sunday, US Secretary of State Antony Blinken met the Crown Prince to address the conflict.
He later described the meeting as “very productive.”
A day earlier, Blinken met with Saudi Arabia’s Foreign Minister Prince Faisal bin Farhan.
“The Secretary and the Foreign Minister discussed continued engagement with regional partners to prevent the spread of conflict in the region and their shared commitment to taking steps to help protect civilians,” the US State Department said.