Nigeria placed the states of Adamawa, Borno and Yobe under emergency rule on May 14, following waves of deadly violence by the insurgent group.
President Goodluck Jonathan sent thousands of troops backed by air support to the northeast to crush the four-year-old Islamist uprising.
The UN toll is the first independent fatality figure to have emerged since the military operation was launched.
"Some 1,224 people have been killed in Boko Haram related attacks" since May, the UN humanitarian agency (OCHA) said in a statement.
The toll includes civilians and military personnel, the UN said. It also likely includes vigilante fighters who have risen up to fight the insurgents.
Defence officials have been widely accused of downplaying the number of people killed in Boko Haram raids.