There has long been a push to change it, and the rule rooted in a strict interpretation of Jewish law is now at the heart of a political battle testing Prime Minister Benjamin Netanyahu's government.
"For Israelis, this is like the tip of the trunk of the elephant," said Batya Kallus, a 59-year-old activist with the Women of the Wall group, which has long fought for equal prayer rights at the historic site.
"It's symbolic. It speaks about exclusion in some ways where other forms of exclusion are less visible and obvious," she said on a recent day at the plaza leading to the wall, where rabbis bow in reverence and visitors stuff bits of paper with prayers on them between its stone blocks.
The controversy has highlighted a sensitive debate among Israelis over the often blurry line between state and religion in a country founded as the nation of the Jewish people.
The Western Wall, in Israeli-annexed east Jerusalem, is the holiest site in which Jews are currently permitted to pray, giving the rules surrounding it heavy symbolic importance.
On the surface, the issue is simple -- and it had seemingly been resolved in January.
Activists and reformers want to create a space where women and men are allowed to pray together at the wall, considered among the last remnants of the second Jewish temple, destroyed by the Romans in 70 AD.
It is contentious because the ultra-Orthodox Jewish establishment, which wields legal power over a range of issues in Israel and has often played a kingmaker role in its politics, views such change as sacrilegious.
Under its reading of Jewish law, mixed prayer is not allowed. Women are also not permitted to lead prayers, though Kallus's group regularly does so at the women's section of the wall to the anger of ultra-Orthodox rabbis.
'Will not compromise'
After years of political and legal disputes, not to mention harassment of women seen as breaking tradition at the wall, a compromise was at last reached in January.
The agreement, approved by Israel's cabinet and labelled historic, laid out a plan to create an egalitarian prayer space away from the men's and women's sections controlled by the ultra-Orthodox.
It was said to have been the result of careful negotiations begun in 2013 involving the government, Women of the Wall and the Western Wall rabbi, among others.
But as word spread that the ultra-Orthodox Jewish parties that form part of Netanyahu's coalition had not prevented the deal, pressure built.
Members of the ultra-Orthodox community, which amounts to between seven and 10 percent of Israel's population, expressed outrage.
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Demanding the deal and other related issues be scrapped, ultra-Orthodox politicians have signalled they could pull out of Netanyahu's coalition, which holds only a one-seat majority in parliament.
"There is a status quo that remained over the years and we wish to preserve it," Health Minister Yaakov Litzman, of the United Torah Judaism alliance of ultra-Orthodox parties, said by email.
"We will not compromise."
That is partly because the issue encompasses much more than prayer at the site.
The ultra-Orthodox are opposed to granting religious authority to Reform and Conservative Jews, whose numbers are limited in Israel but who are numerous in the United States.
Those more liberal streams of Judaism have pushed for an easing of restrictions on matters including conversions, marriage and divorce, which are under ultra-Orthodox control in Israel.
The Conservative and Reform movements joined Women of the Wall in its campaign to create the egalitarian prayer space.
"It gives them a formal position in the most holy place for the Jewish people, and that makes many (ultra-Orthodox) leaders outside politics, those that were not involved in striking the compromise, object to it," said Shuki Friedman, head of the Centre for Religion, Nation and State at the Israel Democracy Institute.
Back to the negotiating table?
Efforts are now underway to reach yet another compromise.
Netanyahu in late March gave the head of his office, David Sharan, 60 days to come up with possible solutions.
Friedman said that, despite their firmness in public, the ultra-Orthodox parties have an interest in finding an agreement to avoid another court battle, with previous decisions having gone against them.
They would also not likely relinquish the power they wield and the benefits they receive under one of the most right-wing governments in Israel's history by causing it to collapse, he said.
As for Women of the Wall, they say they are not willing to renegotiate an agreement reached in good faith.
They are planning another challenge to ultra-Orthodox control on April 24 with a first-ever "women's priestly blessing" at the wall -- a tradition always overseen by men.
"The Western Wall is a deeply symbolic place for Israelis and for Jews," Kallus said.
"And it's a place which has utterly excluded women from any kind of active engagement with Judaism."