A photo caption referred to Hamas gunman Fadi Abu Shkhaydam as a “Palestinian man who was fatally shot by Israeli police after he killed one Israeli and wounded four others.”
The gunman’s victim, 26-year-old Eliyahu Kay, was buried in Jerusalem on Monday.
The article had sparked outrage on social media and criticism from Jewish groups.
Board of Deputies President Marie van der Zyl described the headline as "a highly misleading inversion of what took place" and expressed hope the outlet would publish a prominent correction.
“The incident in question saw a Hamas terrorist kill one Israeli civilian and wound four others, before being neutralised by the Israeli police," she said.
A statement from the Jewish Representative Council of Greater Manchester and Region said it contacted MEN's editor to demand an "urgent meeting."
It also hit out against the regional title for "the framing of the headline and the subsequent article" that "recklessly fails to reflect the tragic incident."