Meeting after midnight in the seaside city, the senior officials spoke for an hour and 40 minutes, a US official said. They discussed the wars in Yemen and Sudan, among other subjects.
“There was a good degree of convergence on potential initiatives where we share the same interests, while also recognising where we have differences,” the official said.
An issue of top priority is the possible normalisation of ties between Saudi Arabia and Israel, even though officials had played down the likelihood of any major progress on the topic.
“They discussed the potential for normalisation of relations with Israel and agreed to continued dialogue on the issue,” the US official said.
America’s top diplomat and the Crown Prince also spoke about “aspects of co-operation in various fields and developments in regional and international situations”, according to the Saudi press agency.
The meeting was attended by Prince Faisal bin Farhan, Saudi Foreign Minister, Princess Reema bint Bandar, the kingdom's ambassador to the US, and Musaed Al Aiban, Saudi Minister of State and National Security Adviser, as well as several US officials.
“The two affirmed their shared commitment to advance stability, security and prosperity across the Middle East and beyond, including through a comprehensive political agreement to achieve peace, prosperity and security in Yemen,” State Department spokesman Matthew Miller said.
The two countries have led talks between the warring sides in Sudan.
“The secretary also thanked the Crown Prince for Saudi Arabia’s support [in] evacuating hundreds of US citizens from Sudan, and for the kingdom’s ongoing partnership in diplomatic negotiations to stop the fighting there,” said Mr Miller.
Mr Blinken and Prince Mohammed also discussed deepening economic co-operation, especially in the clean energy and technology fields, the department said.
Early on Wednesday, Mr Blinken participated in a Sudan evacuation “thank you” event with staff from the US consulate in Jeddah and the embassy in Khartoum.
He is then expected to meet Prince Faisal and attend a meeting with foreign ministers of the Gulf Co-operation Council in Riyadh.
Later, he is to attend a global Coalition to Defeat ISIS ministerial meeting.
Mr Blinken is on a two-day trip to Saudi Arabia as the US tries to shore up ties with a key regional ally.
Relations between the two countries have been frosty under President Joe Biden. However, the US has made overtures in recent months.
In May, White House National Security Adviser Jake Sullivan travelled to the kingdom and met Prince Mohammed.