The palace said Netanyahu and King Abdullah held talks behind closed doors about the "developments in the peace process" and Israeli-Palestinian negotiations sponsored by the U.S.
The visit was not previously announced. Netanyahu made at least three similar visits to Jordan last year. There was no immediate comment in Israel on Thursday's visit.
Jordan maintains cordial relations with Israel under a peace treaty signed in 1994 — one of only two signed agreements the Jewish state has with an Arab nation.
Abdullah's talks with Netanyahu came a week after the king hosted Palestinian President Mahmoud Abbas, and days earlier, U.S. Secretary of State John Kerry.
The palace said the meeting with Netanyahu was significant because it coincided with a "critical period" in the negotiations. The statement did not elaborate.
In the Israeli-Palestinian negotiations, which resumed last summer, the two sides set an April target date for agreeing on a framework for peace. But in recent weeks, they appear to have hardened their positions.
The Palestinians seek the West Bank, east Jerusalem and Gaza Strip, territories captured by Israel in 1967, for an independent state. Netanyahu wants to keep parts of the West Bank and says he will not share control of east Jerusalem, home to sensitive religious sites. He has also insisted that the Palestinians recognize Israel as the Jewish homeland, a condition they say would undermine the rights of Palestinian refugees and Israel's own Arab minority.
Jordan has significant interest in the peace talks, especially in its own border with a future Palestinian state, as well as in the fate of Jerusalem and hundreds of thousands of Palestinians and their descendants displaced to the kingdom in the 1967 Mideast War.
Jordan hosts the largest number of Palestinians outside the West Bank and Gaza.
Also, the peace treaty with Israel recognizes a "special" Jordanian role in caring for Muslim and Christian holy shrines in east Jerusalem, which the Palestinian hope would be the capital of their future state.
The palace said the king's meeting with Netanyahu was part of Jordan's "co-operation with all the sides involved in the peace process."
It said the talks reflected the monarch's "keenness to achieve a tangible progress in Palestinian-Israeli negotiations that would meet the aspirations of the Palestinian people, while at the same time protect higher Jordanian interests."