Basel Ghattas, a Christian member of the Israeli parliament for the Arab Joint List coalition, said on his Facebook page that he visited the site to send a message to Prime Minister Benjamin Netanyahu.
"This morning I entered the Al-Aqsa Mosque in spite of Netanyahu," Ghattas said.
"Israel does not control who is banned from entering the mosque, and continues to change the status quo."
Ghattas posted photos and a video appearing to show him on Wednesday in and around the mosque complex, which is the third-holiest site in Islam and the most sacred for Jews, who refer to it as the Temple Mount.
The ban appeared mainly to target Jewish members of government whose visits to the site are seen as provocation by Palestinians.
Fifty-nine Palestinians and one Arab Israeli have also been killed.
Some of them were shot dead by Israeli police while carrying out attacks, but others have been killed by security forces while taking part in protests.
Muslims accuse Israel of seeking to change rules governing the site and to allow Jews to pray there.
Netanyahu has repeatedly denied plans to change the status quo.
Gilad Erdan, Israel's minister of internal security, slammed Ghattas's visit in a message on his Twitter account.
"The vile provocation of the deputy Basel Ghattas only highlights his inadequacy as a representative of the public. His initiative could incite violence and lead to death," he wrote.
The visit is only the latest in a series of events straining efforts to douse tensions over Al-Aqsa.
On Tuesday, Deputy Foreign Minister Tzipi Hotovely stoked Palestinian fears by saying it was her "dream to see the Israeli flag flying" over the holy site in annexed east Jerusalem.