The United Nations Educational, Scientific and Cultural Organisation committee, which began its annual session in the Cambodian capital Phnom Penh on Sunday, said there had been improvements in the site's management and conservation.
The "remains of the desert citadel, which reached its apogee from the 7th to 11th centuries, had been sufficiently stabilised and its management was sound enough for the site to be declared safe," UNESCO said in a statement.
Iran sits astride several major fault lines and is prone to frequent earthquakes, some of which have been devastating.
The December 2003 quake killed about 26,000 people and largely destroyed the enormous mud-built citadel on the Silk Road.
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UNESCO spokesman Roni Amelan said the committee's decision to remove it from the endangered list reflected a "positive development in (Bam's) safeguarding."
"It is very good news indeed when problems that (are) threatening the outstanding universal value of a site are overcome," he added.
Six ancient Syrian sites as well as Australia's Great Barrier Reef could be added to the endangered list.