According to the Simon Wiesenthal Center, the museum will address "global anti-Semitism, extremism, hate, human dignity and responsibility, and promoting unity and respect among Jews and people of all faiths.

"[6] Unlike the Museum of Tolerance of Los Angeles, the MTJ will not deal with the Holocaust since Yad Vashem in Jerusalem is already dedicated to this purpose.

[1] Another goal of the MTJ is to revive the city center as a venue for theater and music performances, conventions, food and wine festivals, children's events and art workshops.

[4] The rights to their design are owned by the Simon Wiesenthal Center, who entrusted the completion of the project to the Hong Kong-based Aedas architectural firm in cooperation with the Yigal Levy architects' office in Jerusalem.

"[1] The museum's footprint intrudes into the Mamilla Cemetery, which dates back to the time of the Crusades and contains the graves of Islamic figures, as well as several Mamluk tombs.

[17][18] After controversy concerning its location on part of the land of a burial site came to head, the museum's construction was frozen by a Supreme Court order issued in February 2006.

[19] In November 2008, the Israeli Supreme Court allowed construction to proceed, noting that this corner of the cemetery had been transformed into a parking lot "as long ago as the 1960s",[6] and that Jerusalem has been inhabited for roughly 4,000 years, and many ancient sites have been built over.