No incidents occurred as Mr Glick, of Prime Minister Benjamin Netanyahu’s Likud party, toured on Tuesday the Haram al-Sharif mosque compound, known to Jews as the Temple Mount.
Some Muslim worshippers yelled “Allahu akbar” (God is greatest) as he left and he waved to them.
Jews are not allowed to publicly pray at the compound to avoid provoking tensions, but Mr Glick admitted praying to himself as he walked the grounds in his bare feet.
He said he prayed for his wife, who he said was in a coma, as well as his family and Israel.
Asked afterwards whether such visits are provocations that risk more bloodshed, Mr Glick told journalists: “Those who are responsible for terror are the terrorists and those who incite them, not the victims.”
At least one other Jewish lawmaker, Shuli Moalem-Refaeli of the far-right Jewish Home party, also visited on Tuesday morning, according to the Waqf, a Muslim organisation that administers the site.
Jewish lawmakers were allowed to visit in the morning, while Muslim lawmakers were permitted to do so in the afternoon – although they said they did not intend to do so.
Masud Ganaim, of the mostly Arab Joint List alliance, said allowing right-wing politicians into the compound had “the goal of provoking Arab and Muslim sentiment and inflaming the situation”.
Jordan, the custodian of Muslim holy sites in Jerusalem, condemned the visits as “unacceptable”.
Mohammad al-Momani, minister of state for media affairs, said allowing the visits was an “irresponsible decision that will increase tension and escalation at a place holy to all Muslims”.
He called on Israel “as the occupying power to take measures to prevent provocations by extremists against the Al-Aqsa mosque”.
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Mr Netanyahu instructed police in October 2015 to bar lawmakers from visiting the site in the Old City of Israeli-annexed east Jerusalem, which houses the Al-Aqsa mosque complex and the Dome of the Rock.
It was meant to help calm unrest that erupted in part over Palestinian fears that Israel was planning to assert further control over the compound.
Mr Netanyahu has said repeatedly that he is committed to the status quo there.
Plans to allow a temporary lifting of the ban in July were put off after violence again erupted in and around the site.
Tuesday’s one-day lifting of the ban is intended as a test to see if calm can be maintained.
The site is the holiest in Judaism as the location of the two ancient Jewish temples and the third-holiest in Islam after Mecca and Medina.
It is central to the Israeli-Palestinian conflict.
Mr Glick, a US-born rabbi, survived a 2014 assassination attempt by a Palestinian over his campaign for Jewish prayer rights at the site before he joined parliament.